Journal articles on the topic 'Sediment diversity'
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Misson, Benjamin, Cédric Garnier, and Alexandre J. Poulain. "Limited influence of marine sediment lyophilization on prokaryotic community structure assessed via amplicon sequencing: an example from environmentally contrasted sediment layers in Toulon harbor (France)." PeerJ 9 (April 7, 2021): e11075. http://dx.doi.org/10.7717/peerj.11075.
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Sediment lyophilization is a common process that allows for long-term conservation and sharing of marine sediments for multiple downstream analyses. Although it is often used for geochemical studies, the effects of lyophilization on prokaryotic taxonomic diversity assessment remained to be assessed. Here, we tested the effect of lyophilization on microbial diversity assessment using three sediment layers corresponding to various sediment ages and chemical contamination levels sampled from a marine Mediterranean harbor. Duplicate DNA samples were extracted from wet frozen or lyophilized sediments, and 16S rRNA gene amplicon sequence variants were analyzed. We detected changes in community structure over depth linked to both dominant and less abundant taxa whether sediments were lyophilized or not. Data from both wet frozen and lyophilized sediments led us to conclude that historical chemical contamination of the sediment of Toulon Bay did not appear to be the main environmental variable shaping prokaryotic community structure on the vertical dimension, but that sediment diagenesis was. We conclude that sediment lyophilization is compatible with marine biogeochemical and ecotoxicological studies but that caution should be used when discussing small variations among samples.
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Indrayani, Wiwin Try, Haeruddin Haeruddin, and Supriharyono Supriharyono. "Konsentrasi Nitrat dan Fosfat pada Sedimen dan Hubungannya dengan Kelimpahan dan Keanekaragaman Makrozoobentos di Sungai Kreo Semarang Relationship of Nitrate and Phosphate Consetration in Sediments with Macrozoobhentos Abundance and Diversity in Kreo River Semarang." Management of Aquatic Resources Journal (MAQUARES) 9, no. 1 (June 12, 2020): 1–7. http://dx.doi.org/10.14710/marj.v9i1.27752.
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ABSTRAKSungai Kreo merupakan suatu ekosistem yang di dalamnya terdapat beberapa komponen yang saling berinteraksi. Zat hara nitratdan fosfat biasanya terkandung di dalam air dan sedimen. Peranan nitrat dan fosfat yang terkandung dalam sedimen yang ada di sungai adalah sebagai unsur penting bagi pertumbuhan dan kelangsungan mikroorganisme dasar perairan. Tujuan penelitian ini yakni mengetahui konsentrasi nitrat dan fosfat pada sedimen, mengetahui jenis tekstur sedimen, mengetahui kelimpahan dan keanekaragaman makrozoobentos dan menganalisis hubungan konsentrasi nitrat dan fosfat pada sedimen dengan kelimpahan dan Keanekaragaman makrozoobentos di Sungai Kreo Semarang. Metode penelitian yang digunakan adalah metode eksplanatif. Penentuan stasiun sampling menggunakan teknik purposive sampling. Analisis data menggunakan uji regresi linier berganda dengan software SPSS 16. Hasil penelitian menunjukkan bahwa konsentrasi nitrat berkisar 0,14 mg/l - 0,63 mg/l. Konsentrasi fosfat berkisar 0,01 mg/l - 0,11 mg/l. Jenis sedimen stasiun I: lempung liat berpasir, stasiun II: pasir berlempung dan stasiun III : pasir. Spesies Makrozoobentos yang ditemukan adalah kelas gastropoda (Sulcospira sp, Melanoides sp, Brotia sp Annetome sp, Tarebia sp). Keanekaragaman jenis termasuk dalam keanekaragaman yang rendah (0,23 - 0,25). Hubungan konsentrasi nitrat fosfat terhadap kelimpahan dan keanekaragaman termasuk hubungan kuat (r = 0,675). ABSTRACTKreo River is an ecosystem in which there are several interacting components. Nitrate and phosphate nutrients are usually contained in water and sediments. The role of nitrate phosphate contained in sediments in rivers is an important element for the growth and survival of aquatic microorganisms. The purpose of this study was to determine the concentration of nitrate, phosphate sediment and the type of sediment texture in Semarang Kreo River. As well, to investigate the abundance and diversity of macrozoobentos in the Semarang Kreo River, analyzing the relationship of nitrate and phosphate concentrations in sediments with abundance of macrozoobentos in Semarang Kreo River. The study method was used the explanatory method. Sampling was used purposive sampling technique. Data analysised were multiple linear regression test with SPSS 16 software. The results of study showed that the concentration of nitrate was around 0.14 mg/l - 0.63 mg/l. Phosphate concentrations ranged from 0.01 mg/l - 0.11 mg/l. Station I sediment types: sandy clay loam, station II: clay sand and station III: sand. Macrozoobentos genus found were the gastropod class (Sulcospira sp, Melanoides sp, Brotia sp, Annetome sp, Tarebia sp). The diversity of macrozoobentos is included in the low diversity (0,23-0,25). The strong relationship was found between nitrate phosphate concentration and the abundance and diversity (r = 675).
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Helton, Rebekah R., and K. Eric Wommack. "Seasonal Dynamics and Metagenomic Characterization of Estuarine Viriobenthos Assemblages by Randomly Amplified Polymorphic DNA PCR." Applied and Environmental Microbiology 75, no. 8 (February 13, 2009): 2259–65. http://dx.doi.org/10.1128/aem.02551-08.
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ABSTRACT Direct enumeration and genetic analyses indicate that aquatic sediments harbor abundant and diverse viral communities. Thus far, synecological analysis of estuarine sediment viral diversity over an annual cycle has not been reported. This oversight is due in large part to a lack of molecular genetic approaches for assessing viral diversity within a large collection of environmental samples. Here, randomly amplified polymorphic DNA PCR (RAPD-PCR) was used to examine viral genotypic diversity within Chesapeake Bay sediments. Using a single 10-mer oligonucleotide primer for all samples, RAPD-PCR analysis of sediment viral assemblages yielded unique banding patterns across spatial and temporal scales, with the occurrence of specific bands varying among the sample set. Cluster analysis of RAPD-PCR amplicon banding patterns indicated that sediment viral assemblages changed with season and to a lesser extent with geographic location. Sequence analysis of RAPD-PCR amplicons revealed that 76% of sediment viral sequences were not homologous to any sequence in the GenBank nonredundant protein database. Of the GenBank sequence homologs, the majority belonged to viruses within the Podoviridae (24%) and Myoviridae (22%) viral families, which agrees with the previously observed frequencies of these morphological families in Chesapeake Bay sediments. Furthermore, the majority of the sediment viral sequences homologous to GenBank nonredundant protein sequences were phages or prophages (57%). Hence, RAPD-PCR proved to be a reliable and useful approach for characterization of viral assemblages and the genetic diversity of viruses within aquatic sediments.
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Tan, Ling, Hui Yun, Xia Yi Xu, Jia He, Hai Yan Wu, Guan Zhou Qiu, Xin Xing Liu, and Jian Ping Xie. "Comparative Analysis of Functional Gene Diversity of Acid Mine Drainage and its Sediment by Geochip Technology." Solid State Phenomena 262 (August 2017): 531–36. http://dx.doi.org/10.4028/www.scientific.net/ssp.262.531.
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The diversity of microbial community is well studied in past decades, however, the functional gene diversity in AMD and sediment are still unclear. In this study, four samples, which included two mine drainages and two sediments were taken from two typical copper mines in the southeast of China. Community DNA from the AMD and corresponding sediments were were extracted, purified, amplified, labeled and hybridized with GeoChip 2.0. The results showed that total 28, 126, 1131, 1875 functional genes were detected in DX_110, YP_NK, DX_110N, YP_NKN, respectively, which including carbon and nitrogen fixation, carbon degradation, methane metabolism, ammonification, nitrification, denitrification, nitrogen reduction, sulfur reduction and metal resistance genes. Sediment nearby the mine drainage may play an important role in microbial geochemical processes, since more functional genes and higher diversity were detected in sediment than in AMD.
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Weisbrod, Barbara, Susanna A. Wood, Konstanze Steiner, Ruby Whyte-Wilding, Jonathan Puddick, Olivier Laroche, and Daniel R. Dietrich. "Is a Central Sediment Sample Sufficient? Exploring Spatial and Temporal Microbial Diversity in a Small Lake." Toxins 12, no. 9 (September 9, 2020): 580. http://dx.doi.org/10.3390/toxins12090580.
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(1) Background: Paleolimnological studies use sediment cores to explore long-term changes in lake ecology, including occurrences of harmful cyanobacterial blooms. Most studies are based on single cores, assuming this is representative of the whole lake, but data on small-scale spatial variability of microbial communities in lake sediment are scarce. (2) Methods: Surface sediments (top 0.5 cm) from 12 sites (n = 36) and two sediment cores were collected in Lake Rotorua (New Zealand). Bacterial community (16S rRNA metabarcoding), Microcystis specific 16S rRNA, microcystin synthetase gene E (mcyE) and microcystins (MCs) were assessed. Radionuclide measurements (210Pb, 137Cs) were used to date sediments. (3) Results: Bacterial community, based on relative abundances, differed significantly between surface sediment sites (p < 0.001) but the majority of bacterial amplicon sequence variants (88.8%) were shared. Despite intense MC producing Microcystis blooms in the past, no Microcystis specific 16S rRNA, mcyE and MCs were found in surface sediments but occurred deeper in sediment cores (approximately 1950′s). 210Pb measurements showed a disturbed profile, similar to patterns previously observed, as a result of earthquakes. (4) Conclusions: A single sediment core can capture dominant microbial communities. Toxin producing Microcystis blooms are a recent phenomenon in Lake Rotorua. We posit that the absence of Microcystis from the surface sediments is a consequence of the Kaikoura earthquake two years prior to our sampling.
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Coates, John D., Debra J. Ellis, Elizabeth L. Blunt-Harris, Catherine V. Gaw, Eric E. Roden, and Derek R. Lovley. "Recovery of Humic-Reducing Bacteria from a Diversity of Environments." Applied and Environmental Microbiology 64, no. 4 (April 1, 1998): 1504–9. http://dx.doi.org/10.1128/aem.64.4.1504-1509.1998.
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ABSTRACT To evaluate which microorganisms might be responsible for microbial reduction of humic substances in sedimentary environments, humic-reducing bacteria were isolated from a variety of sediment types. These included lake sediments, pristine and contaminated wetland sediments, and marine sediments. In each of the sediment types, all of the humic reducers recovered with acetate as the electron donor and the humic substance analog, 2,6-anthraquinone disulfonate (AQDS), as the electron acceptor were members of the familyGeobacteraceae. This was true whether the AQDS-reducing bacteria were enriched prior to isolation on solid media or were recovered from the highest positive dilutions of sediments in liquid media. All of the isolates tested not only conserved energy to support growth from acetate oxidation coupled to AQDS reduction but also could oxidize acetate with highly purified soil humic acids as the sole electron acceptor. All of the isolates tested were also able to grow with Fe(III) serving as the sole electron acceptor. This is consistent with previous studies that have suggested that the capacity for Fe(III) reduction is a common feature of all members of theGeobacteraceae. These studies demonstrate that the potential for microbial humic substance reduction can be found in a wide variety of sediment types and suggest thatGeobacteraceae species might be important humic-reducing organisms in sediments.
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Steyaert, Maaike, Nelia Garner, Dirk van Gansbeke, and Magda Vincx. "Nematode communities from the North Sea: environmental controls on species diversity and vertical distribution within the sediment." Journal of the Marine Biological Association of the United Kingdom 79, no. 2 (April 1999): 253–64. http://dx.doi.org/10.1017/s0025315498000289.
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Nematode assemblages were sampled seasonally at three subtidal stations along the Belgian coast. The stations were characterized by muddy sediments (station 115), fine sand (station 702) and fine to coarse sand (station 790). The forces structuring vertical distribution were investigated by evaluating abundance, species composition, diversity and trophic composition, and relating these to sediment composition, redox state and food sources.The nematode assemblages at the two finer grained stations (115, 702) were dominated by Daptonema tenuispiculum and Sabatieria punctata. For both species, the vertical distribution in the sediment seemed not dependent on the redoxchemistry, as former believed for S. punctata, but primarily influenced by food availability. This feature could also be recognized for Ixonema sordidum and Viscosia langrunensis, the most abundant nematodes at the coarse sandy station (790).In general, nematode diversity was regulated primarily by sediment granulometry. Coarser sediments (station 790) yielded more diverse communities compared to the fine sediments (station 115, 702), however seasonal fluctuations and variations with depth into the sediment were not obvious. At the silty stations, when the sediment column was more oxidized in March, overall diversity was higher and showed a positive relationship to the mud content which varied with depth into the sediment. This positive relation is probably explained by an enhanced deposition of organic matter associated with the accumulation of fine particles near the river-mouths. Furthermore, the higher abundance, the lower diversity and the higher dominance found at the two silty stations of the eastern and the western part of the Belgian coast, pointed to a stressed, organically enriched environment.The results demonstrate that controls on nematode community structure are complex and that information at both species and community level are required to properly evaluate the effects of natural and anthropogenic impacts.
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Najah, Safirotun, Haeruddin Haeruddin, and Arif Rahman. "Hubungan Zat Hara (HNO3- dan HPO4-) pada Sedimen terhadap Kelimpahan dan Keanekaragaman Makrozoobentos di Kaligarang, Semarang Relationship between Sediment Fertility And Macrozoobenthos Abundance and Diversity in the Kaligarang, Semarang." Management of Aquatic Resources Journal (MAQUARES) 9, no. 1 (June 12, 2020): 31–39. http://dx.doi.org/10.14710/marj.v9i1.27757.
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ABSTRAK Kaligarang merupakan sungai yang berada diantara pemukiman penduduk yang menghasilkan limbah rumah tangga. Limbah tersebut merupakan sumber nitrat dan fosfat yang mempengaruhi kesuburan sedimen sungai. Peran nitrat dan fosfat dalam sedimen yaitu sebagai unsur hara yang secara tidak langsung dibutuhkan makrozoobentos untuk kelangsungan hidupnya. Faktor yang mempengaruhi secara langsung yaitu bahan organik dan tekstur sedimen. Tujuan penelitian ini adalah mengetahui konsentrasi nitrat dan fosfat dalam sedimen perairan Kaligarang. Mengetahui kelimpahan dan keanekaragaman makrozoobentos di Kaligarang. Menganalisis konsentrasi nitrat dan fosfat pada sedimen dengan kelimpahan dan keanekaragaman makrozoobentos di Kaligarang. Penelitian ini dilakukan 2 kali pada bulan Juni 2019 dengan metode purposive sampling. Variabel yang diukur yaitu tekstur sedimen, nitrat dan fosfat, bahan organik total, pH sedimen, oksigen terlarut, dan alkalinitas. Analisis data menggunakan analisis regresi linear sederhana dengan software SPSS 16. Hasil penelitian yang telah dilakukan konsentrasi nitrat berkisar 0,19 – 0,35 mg/l dan konsentrasi fosfat berkisar 0,05 – 0,17 mg/l . Makrozoobentos yang ditemukan Clea Helena, Melanoides sp., Mieniplotia sp., dan Tarebia sp. Kelimpahan yang tertinggi yaitu C. helena senilai 4044 dan kelimpahan terendah Mieniplotia sp. senilai 44 individu/m2. Indeks keanekaragaman makrozoobentos 0,26 – 0,89. Hubungan nitrat dengan kelimpahan makrozoobentos dengan r=0,99 tergolong tinggi, korelasi fosfat dengan kelimpahan makrozoobentos yaitu r=0,38 yang tergolong rendah. Korelasi nitrat dengan keanekaragaman makrozoobentos tergolong rendah dengan r =0,18 dan korelasi fosfat dengan keanekaragaman makrozoobentos tergolong tinggi dengan r =0,87. ABSTRACT Kaligarang is a river that is located in a residential area that produces an household waste. The waste is a source of nitrate and phosphate which give an affect the fertility of river sediments. The role of nitrate and phosphate in sediments is as a nutrient needed by microorganisms for survival. The purpose of this study is to determine the concentration of nitrate and phosphate in Kaligarang waters sediments, Know the abundance and diversity of macrozoobenthos in Kaligarang and analyze the relationship of sediment fertility with abundance and diversity of macrozoobenthos in Kaligarang. The research has be done two samplings in June 2019 with a purposive sampling method. The measured variables are sediment texture, nitrate and phosphate, total organic matter, pH sediment, dissolved oxygen, and alkalinity. Data analysis using multiple linear regression analysis with SPSS 16 software. The results of studies that have been carried out nitrate concentrations ranged from 0,19 – 0,35 mg /l and phosphate concentrations ranged from 0,05 – 0,17 mg /l. Macrozoobentos found by Clea helena, Melanoides sp., Mieniplotia sp., and Tarebia sp. The highest abundance was C. helena with a value of 4044 and the lowest abundance with Mieniplotia sp with 44 individuals / m2. Diversity index macrozoobentos of 0,26 – 0,89. The correlation of nitrate correlation with abundance macrozoobentos of 0,99 is classified as high, the correlation of phosphate with abundance macrozobentos of r=0,38 is classified as low. The correlation of nitrate with diversity mcrozoobentos is low r= 0.18 and phosphate correlation with diversity macrozoobentos is high with r=0,87.
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Ariawan, Febio, Haeruddin Haeruddin, and Arif Rahman. "HUBUNGAN ZAT HARA (HNO3-DAN PO4-) SEDIMEN TERHADAP KELIMPAHAN DAN KEANEKARAGAMAN MAKROZOOBENTOS DI SUNGAI BANJIR KANAL BARAT, SEMARANG Relationship between Sediment Fertility and Macrozoobenthos Abundance and Diversity in the Banjir Kanal Barat River, Semarang." Management of Aquatic Resources Journal (MAQUARES) 8, no. 4 (January 28, 2020): 300–308. http://dx.doi.org/10.14710/marj.v8i4.26548.
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Sungai Banjir Kanal Barat membutuhkan perhatian serius dari berbagai elemen masyarakat, dikarenakan sungai ini banyak digunakan oleh masyarakat. Kandungan nutrien yang ada di sedimen berpengaruh terhadap keanekaragaman dan kelimpahan makrozoobentos jika semakin berlimpah dan beranekaragam maka sungai itu memiliki kesuburan yang tinggi. Tujuan penelitian ini untuk mengetahui tekstur, konsentrasi nitrat dan fosfat pada sedimen, kelimpahan dan keanekaragaman makrozoobentos serta hubungan antara kesuburan pada sedimen dengan kelimpahan dan keanekaragaman makrozoobentos di Sungai Banjir Kanal Barat, Semarang. Penelitian ini dilaksanakan pada bulan April-Mei 2019 menggunakan teknik purposive sampling dengan total 5 stasiun. Sampel yang diambil berupa sedimen dan makrozoobentos. Metode penentuan sedimen menggunakan metode pemipetan, nitrat fosfat menggunakan spektrofotometri, untuk mengetahui hubungan antara kesuburan dengan kelimpahan dan keanekaragaman menggunakan metode PCA. Hasil penelitian yang telah dilakukan menerangkan bahwa fraksi sand berkisar 10,84-92,04%; fraksi silt berkisar antara 0-70%; fraksi clay berkisar antara 2,80-25,48%. Genus makrozoobentos yang ditemukan dikelompokan menjadi 2 kelas yaitu: Gastropoda (Afropomus sp., Melanoides sp., Terebia sp., Terebra sp., Urosalpinx sp.) dan Bivalvia (Anadara sp., Corbicula sp., Leiosolenussp.). Keanekaragaman jenis makrozoobentos berkisar antara 0,45-1,96 dan termasuk dalam kategori rendah. Kelimpahan individu berkisar antara 15200-42800 ind/m³ dan kelimpahan tertinggi terdapat pada stasiun IV dan stasiun II merupakan kelimpahan terendah. Konsentrasi nitrat dan fosfat sedimen berkisar antara 0,04-0,60 mg/l untuk nitrat lalu konsentrasi fosfat berkisar antara 0,03-1,33 mg/l. Analisis PCA menyatakan konsentrasi nitrat pada sedimen berpengaruh terhadap makrozoobentos. konsentrasi nitrat di sedimen cukup berpengaruh dengan keanekaragaman jenis dan kelimpahan makrozoobentos yang ada diperairan, dan memiliki nilai koefisien korelasi sebesar 0,99 dan 0,87. The Banjir Kanal Barat River needs serious attention from various elements of the community, because the river is widely used by the community. Nutrient content in sediments affects the diversity and abundance of macrozoobenthos. The concentration of nitrate and phosphate in the sediment are used phytopentos, phytopentos is benthic food. macrozoobenthos is a bioindicator of water, if it is more abundant and diverse, the river has high fertility. The purpose of this study was to determine the texture, nitrate and phosphate concentrations in sediments, abundance and diversity of macrozoobenthos and the relationship between fertility in sediments with abundance and diversity of macrozoobenthos in the West Flood River Canal, Semarang. This research was conducted in April-May 2019 using a purposive sampling technique with a total of 5 stations. Samples taken in the form of sediments and macrozoobenthos. The results of the research that have been done explained that the sand fraction ranged from 10.84 to 92.04%; silt fraction ranges from 0-70%; clay fraction ranged from 2.80-25.48%. The macrozoobenthos genus found was classified into 2 classes, namely: Gastropods (Afropomus sp., Melanoides sp., Terebia sp., Terebra sp., Urosalpinx sp.) And Bivalvia (Anadara sp., Corbicula sp., Leiosolenus sp.). Diversity of macrozoobenthos types ranged from 0.45 to 1.96 and included in the low category. Individual abundances ranged from 15200 to 42800 ind / m³ and the highest abundances were at station IV and station II was the lowest abundance. Nitrate and phosphate sediment concentrations ranged from 0,04 to 0,60 mg / l for nitrates and then phosphate concentrations ranged from 0,03 to 1,33 mg / l. PCA analysis resulted that the concentration of nitrate in the sediment affected macrozoobenthos. Nitrate concentration in sediments is quite influential with the diversity of species and abundance of macrozoobenthos in the water, and has a correlation coefficient of 0,99 and 0,87.
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Smorczewski, W. T., and E. L. Schmidt. "Numbers, activities, and diversity of autotrophic ammonia-oxidizing bacteria in a freshwater, eutrophic lake sediment." Canadian Journal of Microbiology 37, no. 11 (November 1, 1991): 828–33. http://dx.doi.org/10.1139/m91-143.
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The microbiological and chemical potential for ammonia oxidation in a freshwater, eutrophic lake sediment was examined in relation to environmental changes caused by seasonal, dimictic circulation. Poulations of both ammonia and nitrite oxidizers as estimated by most probable number (MPN) were sustained throughout extended anaerobic summer intervals, with nitrite oxidizers outnumbering ammonia oxidizers by a factor ranging from 3.0 to 8.1. Ammonia oxidation potential on a per cell basis was affected by seasonal changes and was seen to decrease as oxygen was removed from the sediments. Pure-culture isolations from a positive MPN tube inoculated with oxygenated sediment and representing a single point in a seasonal cycle produced ammonia-oxidizing strains belonging to the genus Nitrosospira. These strains did not react with known ammonia-oxidizer serotypes and, therefore, extend the serological diversity of this group of bacteria. An immunofluorescence analysis of MPN tubes from sediment collected during a period of lake stratification revealed progressive changes in the diversity of the ammonia-oxidizer population. The genera Nitrosomonas, Nitrosolobus, and Nitrosospira, including the novel serotype of Nitrosospira isolated from the sediment a year earlier, were found to coexist in well-oxygenated sediment. This diversity was seen to disappear, with Nistrosomonas surviving, as anaerobic conditions persisted. Key words: ammonia oxidizers, lake sediments, nitrifiers, nitrification.
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Pham, Huynh A., Carolyn E. Oldham, and Jason J. Plumb. "The Diversity of Benthic Microorganisms in Acidic Mine Lake Sediments." Advanced Materials Research 20-21 (July 2007): 489–92. http://dx.doi.org/10.4028/www.scientific.net/amr.20-21.489.
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The sediment microbial communities of a disused coal mine lake, Lake Kepwari (pH~4.5-5) were studied to understand how the natural microbial processes in an oligotrophic acidic mine lake system influence the iron and sulphur cycles. Most probable number (MPN) viable counts were used to enumerate the benthic bacteria at different depths. MPN results revealed an abundance of bacteria that were capable of growing in sulphate reducing medium with numbers in the range of 1 × 107 – 1 × 108 cells.g-1 of wet sediment. In contrast, MPN results showed much lower numbers of bacteria that were capable of growing in ferric reducing medium with 1 × 102 – 2 × 103 cells.g-1 of wet sediment detected. Serial decimal dilution cultures were used to isolate pure strains of benthic bacteria. Strains HP1, HP2 and HP3 were isolated from benthic lake sediments at 18 m, 0 m and 10 m water depths respectively. 16S rRNA gene sequence analysis of strain HP1 showed that the strain belonged to the genus Enterobacter, strain HP2 belonged to the Order Rhizobiales and strain HP3 belonged to the sub-order Micrococcineae. Denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene fragments was used to profile the diversity of the benthic microbial communities at different depths. DGGE profiling of benthic sediments revealed that sediments contained mostly members of the Proteobacteria, Actinobacteria and Firmicutes phyla.
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Kretz, Lena, Katinka Koll, Carolin Seele-Dilbat, Fons van der Plas, Alexandra Weigelt, and Christian Wirth. "Plant structural diversity alters sediment retention on and underneath herbaceous vegetation in a flume experiment." PLOS ONE 16, no. 3 (March 18, 2021): e0248320. http://dx.doi.org/10.1371/journal.pone.0248320.
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Sediment retention is a key ecosystem function provided by floodplains to filter sediments and nutrients from the river water during floods. Floodplain vegetation is an important driver of fine sediment retention. We aim to understand which structural properties of the vegetation are most important for capturing sediments. In a hydraulic flume experiment, we investigated this by disentangling sedimentation on and underneath 96 vegetation patches (40 cm x 60 cm). We planted two grass and two herb species in each patch and conducted a full-factorial manipulation of 1) vegetation density, 2) vegetation height, 3) structural diversity (small-tall vs tall-tall species combinations) and 4) leaf pubescence (based on trait information). We inundated the vegetation patches for 21 h in a flume with silt- and clay-rich water and subsequently measured the amount of accumulated sediment on the vegetation and on a fleece as ground underneath it. We quantified the sediment by washing it off the biomass and off the fleece, drying the sediment and weighting it. Our results showed that all manipulated vegetation properties combined (vegetation density and height, and the interaction of structural diversity and leaf pubescence) explained sedimentation on the vegetation (total R2 = 0.34). The sedimentation underneath the vegetation was explained by the structural diversity and the leaf pubescence (total R2 = 0.11). We further found that vegetation biomass positively affected the sedimentation on and underneath the vegetation. These findings are crucial for floodplain management strategies with the aim to increase sediment retention. Based on our findings, we can identify management strategies and target plant communities that are able to maximize a floodplain’s ability to capture sediments.
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Pester, Michael, Michael W. Friedrich, Bernhard Schink, and Andreas Brune. "pmoA-Based Analysis of Methanotrophs in a Littoral Lake Sediment Reveals a Diverse and Stable Community in a Dynamic Environment." Applied and Environmental Microbiology 70, no. 5 (May 2004): 3138–42. http://dx.doi.org/10.1128/aem.70.5.3138-3142.2004.
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ABSTRACT Diversity and community structure of aerobic methane-oxidizing bacteria in the littoral sediment of Lake Constance was investigated by cloning analysis and terminal restriction fragment length polymorphism (T-RFLP) fingerprinting of the pmoA gene. Phylogenetic analysis revealed a high diversity of type I and type II methanotrophs in the oxygenated uppermost centimeter of the sediment. T-RFLP profiles indicated a high similarity between the active methanotrophic community in the oxic layer and the inactive community in an anoxic sediment layer at a 10-cm depth. There were also no major changes in community structure between littoral sediment cores sampled in summer and winter. By contrast, the fingerprint patterns showed substantial differences between the methanotrophic communities of littoral and profundal sediments.
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Nold, Stephen C., Joseph B. Pangborn, Heidi A. Zajack, Scott T. Kendall, Richard R. Rediske, and Bopaiah A. Biddanda. "Benthic Bacterial Diversity in Submerged Sinkhole Ecosystems." Applied and Environmental Microbiology 76, no. 1 (October 30, 2009): 347–51. http://dx.doi.org/10.1128/aem.01186-09.
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ABSTRACT Physicochemical characterization, automated ribosomal intergenic spacer analysis (ARISA) community profiling, and 16S rRNA gene sequencing approaches were used to study bacterial communities inhabiting submerged Lake Huron sinkholes inundated with hypoxic, sulfate-rich groundwater. Photosynthetic cyanobacterial mats on the sediment surface were dominated by Phormidium autumnale, while deeper, organically rich sediments contained diverse and active bacterial communities.
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Jiang, Hongchen, Hailiang Dong, Gengxin Zhang, Bingsong Yu, Leah R. Chapman, and Matthew W. Fields. "Microbial Diversity in Water and Sediment of Lake Chaka, an Athalassohaline Lake in Northwestern China." Applied and Environmental Microbiology 72, no. 6 (June 2006): 3832–45. http://dx.doi.org/10.1128/aem.02869-05.
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ABSTRACT We employed culture-dependent and -independent techniques to study microbial diversity in Lake Chaka, a unique hypersaline lake (32.5% salinity) in northwest China. It is situated at 3,214 m above sea level in a dry climate. The average water depth is 2 to 3 cm. Halophilic isolates were obtained from the lake water, and halotolerant isolates were obtained from the shallow sediment. The isolates exhibited resistance to UV and gamma radiation. Microbial abundance in the sediments ranged from 108 cells/g at the water-sediment interface to 107 cells/g at a sediment depth of 42 cm. A major change in the bacterial community composition was observed across the interface. In the lake water, clone sequences affiliated with the Bacteroidetes were the most abundant, whereas in the sediments, sequences related to low G+C gram-positive bacteria were predominant. A similar change was also present in the archaeal community. While all archaeal clone sequences in the lake water belonged to the Halobacteriales, the majority of the sequences in the sediments were related to those previously obtained from methanogenic soils and sediments. The observed changes in the microbial community structure across the water-sediment interface were correlated with a decrease in salinity from the lake water (32.5%) to the sediments (approximately 4%). Across the interface, the redox state also changed from oxic to anoxic and may also have contributed to the observed shift in the microbial community.
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Haeruddin, Haeruddin, Supriharyono Supriharyono, Abdul Ghofar, and Arif Rahman. "The Integrated Quality Analysis of Sediment on BanjirKanal Barat River as the Basis of River Environment Management." Current World Environment 14, no. 3 (December 12, 2019): 463–75. http://dx.doi.org/10.12944/cwe.14.3.14.
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There have been many studies on the pollution status of Banjir Kanal Barat (BKB) River; however, many of them are limited to the concentration of metals in the river water and their biodiversity of water biota, and partial analysis. The study aims to analyse the metal concentration in BKB river sediment, its toxic to water biota and the effect on the abundance and diversity of macrozoobenthos. The evaluation of pollution status is conducted with three components integrated approach. The sediments were collected from three sampling stations with three replications. While the community observation included abundance, diversity, evenness and dominance of macrozoobenthos. Toxicity testing had been carried out to observe the inhibition of the growth of Chlorella sp algae in pore water sediments and failure reburial of blood clams into the substrate/sediment. While the evaluation of pollution status was conducted in an integrated three components approach. The results showed that the concentrations of various metals in the sediment were varied. The concentration of metals in sediments were still within natural limits and identical to the reference station that was not polluted. The types of macrozoobenthos were found about nine genera with varying in abundance, diversity index, evenness index, and dominance index. The abundance, diversity index, evenness index, dominance index of macrozoobenthos at all stations were still identical with reference stations, which known was not polluted. Although pore water sediments and sediments from various stations caused inhibition of the growth of Chlorella sp and the failure reburial of blood clams, statistically analysis was not significantly different from the reference station. Overall it can be stated that the sediment quality in those three stations was still excellent, however, they need to be maintained.
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Wang, Juanjuan, Siwen Zhang, Tianyang Que, Anna H. Kaksonen, Xiaoqing Qian, Xuliang Zhuang, and Tsing Bohu. "Mitigation of Eutrophication in a Shallow Lake: The Influences of Submerged Macrophytes on Phosphorus and Bacterial Community Structure in Sediments." Sustainability 13, no. 17 (September 1, 2021): 9833. http://dx.doi.org/10.3390/su13179833.
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Remediating water eutrophication is critical for maintaining healthy and sustainable development of lakes. The aim of this study was to explore the seasonal variation in phosphorus (P) speciation and bacterial community structure in sediments of Qin Lake (Taizhou, Jiangsu Province, China) associated with the growth of submerged macrophyte Vallisneria natans. The differences in sediment bacterial diversity and community structure between V. natans growing and control areas were analyzed over a period of one year. The results showed that V. natans growth reduced the total P and organic matter contents of the sediments and increased the bioavailable iron (Fe) and Fe-bound P contents. The α-diversity of sediment bacteria was significantly higher in the presence of V. natans than in the controls during the vigorous plant growth stage. In the presence of V. natans, there was a higher relative abundance of Proteobacteria and lower relative abundances of Chloroflexi and Acidobacteria. The Fe(II) content in the sediment had a larger influence on the spatial distribution of bacterial communities than sediment Fe-bound P, organic matter, and Fe(II) contents. V. natans growth could reshape sediment bacterial community structure in the shallow lake, which, in turn, enhanced P immobilization in the sediments and thereby improved the water quality.
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Wang, Yu, Hua-Fang Sheng, Yan He, Jin-Ya Wu, Yun-Xia Jiang, Nora Fung-Yee Tam, and Hong-Wei Zhou. "Comparison of the Levels of Bacterial Diversity in Freshwater, Intertidal Wetland, and Marine Sediments by Using Millions of Illumina Tags." Applied and Environmental Microbiology 78, no. 23 (September 21, 2012): 8264–71. http://dx.doi.org/10.1128/aem.01821-12.
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ABSTRACTSediment, a special realm in aquatic environments, has high microbial diversity. While there are numerous reports about the microbial community in marine sediment, freshwater and intertidal sediment communities have been overlooked. The present study determined millions of Illumina reads for a comparison of bacterial communities in freshwater, intertidal wetland, and marine sediments along Pearl River, China, using a technically consistent approach. Our results show that both taxon richness and evenness were the highest in freshwater sediment, medium in intertidal sediment, and lowest in marine sediment. The high number of sequences allowed the determination of a wide variety of bacterial lineages in all sediments for reliable statistical analyses. Principal component analysis showed that the three types of communities could be well separated from phylum to operational taxonomy unit (OTU) levels, and the OTUs from abundant to rare showed satisfactory resolutions. Statistical analysis (LEfSe) demonstrated that the freshwater sediment was enriched withAcidobacteria,Nitrospira,Verrucomicrobia,Alphaproteobacteria, andBetaproteobacteria. The intertidal sediment had a unique community with diverse primary producers (such asChloroflexi,Bacillariophyta,Gammaproteobacteria, andEpsilonproteobacteria) as well as saprophytic microbes (such asActinomycetales,Bacteroidetes, andFirmicutes). The marine sediment had a higher abundance ofGammaproteobacteriaandDeltaproteobacteria, which were mainly involved in sulfate reduction in anaerobic conditions. These results are helpful for a systematic understanding of bacterial communities in natural sediment environments.
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Yuliana, Eka Yulfa, Norma Afiati, and Max Rudolf Muskananfola. "Analisis Kelimpahan Bivalvia di Pantai Prawean Bandengan, Jepara berdasarkan Tekstur Sedimen dan Bahan Organik Abundance Analysis of Bivalve in Prawean Beach, Bandengan, Jepara Based on Sediment and Organic Materials." Management of Aquatic Resources Journal (MAQUARES) 9, no. 1 (June 12, 2020): 47–56. http://dx.doi.org/10.14710/marj.v9i1.27759.
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ABSTRAK Sedimen dan bahan organik berperan penting dalam kehidupan Bivalvia di lingkungan pantai. Sedimen merupakan tempat untuk menempel dan berjalan organisme, sedangkan bahan organik merupakan sumber nutrien. Karakteristik sedimen akan mempengaruhi morfologi, fungsional, tingkah laku serta nutrien. Penelitian ini dilaksanakan pada bulan Juli 2019 di Pantai Prawean Bandengan, Jepara. Tujuan dari penelitian ini adalah mengetahui kelimpahan dan keanekaragaman Bivalvia, tekstur sedimen dan bahan organik serta hubungan kelimpahan Bivalvia terhadap tekstur sedimen dan bahan organik. Metode yang digunakan yaitu deskriptif dengan teknik purposive random sampling. Analisis data menggunakan IBM SPSS Statistics 16. Hasil penelitian diperoleh 3 spesies Bivalvia di Pantai Prawean Bandengan yaitu Anadara antiquata, Gafrarium divaricatum dan Gafrarium tumidum dengan kelimpahan individu sebesar 45 ind/100 m2; 29 ind/100 m2 dan 64 ind/100 m2. Keanekaragaman pada stasiun I (d’Season Premiere), II (Julie Hotel), III (tambak), IV (padang lamun) dan V (pemukiman) berkisar 0,76 – 1,01 dengan kategori rendah sampai sedang. Tekstur sedimen pada stasiun I, II, IV dan V yaitu pasir berlempung sedangkan stasiun III yaitu lempung liat berpasir. Kandungan bahan organik sedimen berkisar 3,696 – 7,846% tergolong rendah. Gangguan lingkungan akibat aktivitas manusia dalam memanfaatkan sumber daya alam secara terus menerus dapat mengancam kestabilan komunitas, sebagaimana diperkirakan oleh hasil penelitian ini khususnya dilihat dari komunitas malacofauna (Bivalvia) yaitu keanekaragaman rendah, keseragaman tinggi dan tidak ada spesies yang mendominasi di substrat pasir berlempung yang kandungan bahan organiknya rendah. Hubungan tekstur sedimen dengan Bivalvia fraksi pasir, lumpur dan liat berkorelasi rendah, sedangkan hubungan kandungan bahan organik dengan Bivalvia berkorelasi kuat. ABSTRACT Sediments and organic material have an essential role for grain size Bivalvia's life in the coastal environment. Sediment is a place for attaching and crawling or benthic organisms, while organic material is a source of nutrients. Sediment characteristics will be affected morphology, functional, behaviour and nutrients. This research was conducted in July 2019 at Prawean Bandengan Beach, Jepara. The purpose of this research was to determine the abundance and diversity of Bivalvia, texture of sediments and organic material and the relationship of Bivalvia abundance for texture of sediment and organic material. The method was used the descriptive with a purposive random sampling technique. Data analysis was conducted using IBM SPSS Statistics 16. The results obtained were three species of Bivalves in Prawean Bandengan Beach namely Anadara antiquata, Gafrarium divaricatum and Gafrarium tumidum with an abundance of individuals of 45 ind/100 m2; 29 ind/100 m2 and 64 ind/100 m2. Diversity values at stations I, II, IV and V ranged from 0.76 to 1.01 in the low to moderate categories. Sediment texture at stations I (d’season premiere), II (Julie hotel), III (ponds), IV (seagrass fields) and V (residents) was clay sand while station IIIwas sandy clay loam. The content of organic sediment was around 3.696 – 7.846% with a low category. Environmental disturbances as impact of human activities in utilising natural resources can affect the stability of a community, as predicted by the results of this study, especially seen from the community of malacofauna (Bivalvia),diversity is low, high uniformity and no species that dominate in the sandy substrate that contains low organic matter. The relationship of sediment texture with Bivalvia sand silt and clay fractions were low correlated, while the relationship of organic material content with Bivalvia was strongly correlated.
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Mills, Heath J., Evan Hunter, Mike Humphrys, Lee Kerkhof, Lora McGuinness, Markus Huettel, and Joel E. Kostka. "Characterization of Nitrifying, Denitrifying, and Overall Bacterial Communities in Permeable Marine Sediments of the Northeastern Gulf of Mexico." Applied and Environmental Microbiology 74, no. 14 (May 16, 2008): 4440–53. http://dx.doi.org/10.1128/aem.02692-07.
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ABSTRACT Sandy or permeable sediment deposits cover the majority of the shallow ocean seafloor, and yet the associated bacterial communities remain poorly described. The objective of this study was to expand the characterization of bacterial community diversity in permeable sediment impacted by advective pore water exchange and to assess effects of spatial, temporal, hydrodynamic, and geochemical gradients. Terminal restriction fragment length polymorphism (TRFLP) was used to analyze nearly 100 sediment samples collected from two northeastern Gulf of Mexico subtidal sites that primarily differed in their hydrodynamic conditions. Communities were described across multiple taxonomic levels using universal bacterial small subunit (SSU) rRNA targets (RNA- and DNA-based) and functional markers for nitrification (amoA) and denitrification (nosZ). Clonal analysis of SSU rRNA targets identified several taxa not previously detected in sandy sediments (i.e., Acidobacteria, Actinobacteria, Chloroflexi, Cyanobacteria, and Firmicutes). Sequence diversity was high among the overall bacterial and denitrifying communities, with members of the Alphaproteobacteria predominant in both. Diversity of bacterial nitrifiers (amoA) remained comparatively low and did not covary with the other gene targets. TRFLP fingerprinting revealed changes in sequence diversity from the family to species level across sediment depth and study site. The high diversity of facultative denitrifiers was consistent with the high permeability, deeper oxygen penetration, and high rates of aerobic respiration determined in these sediments. The high relative abundance of Gammaproteobacteria in RNA clone libraries suggests that this group may be poised to respond to short-term periodic pulses of growth substrates, and this observation warrants further investigation.
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Zallesa, Sheilla, Kresna Tri Dewi, and Noor C. D. Aryanto. "THE CORRELATION BETWEEN BENTHIC FORAMINIFERA AND SEDIMENT TYPES OF SOUTH MAKASSAR STRAIT." BULLETIN OF THE MARINE GEOLOGY 29, no. 2 (February 15, 2016): 53. http://dx.doi.org/10.32693/bomg.29.2.2014.65.
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South Makassar Strait is located between Kalimantan and Sulawesi Islands that is an important oceanographic pathway connecting between the Pacific and Indian oceans. This area is a part of sedimentary basin that has specific seabed morphology and sediment characteristics, including foraminifera as a component of sediments. The purpose of this study is to determine community structure of benthic foraminifera related to sediment characteristics. This study used 20 top core sediment samples from water depth between 200 and 1500 m. There are identified 38 species of benthic foraminifera and some of them are characterized the study area: Anomalinoides colligerus, Lenticulina suborbicularis, Planulina wuellerstorfi, , and Pseudonodosaria discrete. The diversity index is categorized as moderate values (1.0=H'= 3) and the average of evenness values is about 0.79. The dominance values are less than 0.5 indicate that there is no dominant species in the study area. In relation to sediment characteristics, it shows that the high abundance of benthic foraminifera occurs in sediment type of silty sand and sandy silt. Moderate abundance appears in sand following by low abundance in silt and sandy silt sediment types.
Keywords: benthic foraminifera, community structure, sediment types and Makassar Strait
Makassar bagian selatan terletak diantara Pulau Kalimantan dan Sulawesi yang merupakan jalur oseanografik yang penting menghubungkan Samudera Pasifik dan. Wilayah ini merupakan bagian dari cekungan sedimen yang mempunyai morfologi dasar laut dan karakteristik sedimen tertentu termasuk foraminifera sebagai komponen sedimen. Tujuan dari penelitian ini adalah untuk mengetahui struktur komunitas foraminifera bentik dalam kaitannya dengan tipe sedimen dasar laut. Penelitian ini menggunakan 20 sampel sedimen bagian atas dari pemercontoh inti pada kedalaman antara 200 dan 1500 m. Ada 38 spesies foraminifera bentik dan beberapa diantaranya mencirikan daerah penelitian: Anomalinoides colligerus, Lenticulina suborbicularis, Planulina wuellerstorfi, dan Pseudonodosaria discrete. Indeks keanekaragaman termasuk dalam kategori sedang (1,0=H’=3) dan nilai rata-rata keseragaman sekitar 0,79. Nilai dominasi lebih kecil dari 0,5 itu menandakan tidak ada spesies yang dominan pada lokasi penelitian. Terkait dengan karakteristik sedimen menunjukkan bahwa kelimpahan foraminifera bentik tinggi terdapat pada jenis sedimen pasir lanauan dan lanau pasiran. Kelimpahan sedang ditemukan pada jenis sedimen pasir diikuti kelimpahan rendah yang dijumpai pada sedimen lanau dan lanau pasiran. Kata kunci: foraminifera bentik, struktur komunitas, jenis sedimen, Selat Makassar.
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Cheam, V., T. Reynoldson, G. Garbai, J. Rajkumar, and D. Milani. "Local Impacts of Coal Mines and Power Plants across Canada. II. Metals, Organics and Toxicity in Sediments." Water Quality Research Journal 35, no. 4 (November 1, 2000): 609–32. http://dx.doi.org/10.2166/wqrj.2000.035.
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Abstract A Canada-wide survey was undertaken to study local impacts of coal mines and coal-fired electrical generating stations. The first part dealt with thallium in waters and sediments. This, Fart II, deals with metals and organics in sediments as well as sediment toxicity to four different organisms. Several elevated metal and PAH concentrations as well as high toxicity (based on biological sediment guidelines) were observed compared to uncontaminated sites. Based on Ontario's sediment guidelines, most of the studied sediments fell in the "marginally to significantly polluted" category of sediment quality, although two belonged to the "grossly polluted" class due to the extremely high concentrations of some metals. The observed diversity of PAHs and near-unity carbon preference indices indicate non-biological origins of the studied sediments. In this initial study, four different organisms, Chironomus riparius, Hyalella azteca, Hexagenia spp. (Hexagenia limbata) and Tubifex tubifex were used to determine sediment toxicity, which showed 50% of the tested sites were highly stressed.
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Deng, Chen, Oscar Donde, and Ze Qing Li. "Microbial community diversity and eco-genomics functions across sediment regimen of a saline lake." International Journal of Limnology 58 (2022): 10. http://dx.doi.org/10.1051/limn/2022008.
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Unlike most saline lakes, the Chinese ones were formed in depressions entirely by runoff from the surrounding topography, hence greatly affected by seasons and variation in salinity, with microbial composition and functions being the most influenced. Determining the nature of key environmental drivers such as microbial dynamics is necessary. Therefore, the current study applied metagenomics study approach to determining the microbial community diversity and functions across sediment regimen (clay [NT], sandstone [FS] and salt-bearing [SY]) of the East Taijinar Salt Lake, China. The result indicated that members of Actinobacterium did not exhibit variability across the sediment types while members of Firmicutes and Proteobacteria showed some variabilities, and had highest dominance in clay (NT) and sandstone (FS) sediment type as compared to the salt-bearing (SY) sediment type. Based on UniFrac, STAMP analyses there was significant differences (P < 0.05), with the weighted-UniFrac approach indicating the highest abundance under the clay sediment type. According to NMDS analysis, there was closer similarity in microbial composition between the clays sediment type (NT) and sandstone (FS). Furthermore, through the cladogram, it was visualized that there was very low representation of bacterial species from the salt-bearing (SY) sediment type as compared to other sediment types. More COG and KEGG pathways were dominant under the clays (NT) sandstone (FS) sediment types as opposed to the salt-based (SY) sediment type. Based on this result, in-depth studies on spatial and temporal variability in microbial community diversity and eco-genomics functions across the sediments of the East Taijinar Salt Lake is recommended.
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Wang, Juanjuan, Susann Vollrath, Thilo Behrends, Paul L. E. Bodelier, Gerard Muyzer, Marion Meima-Franke, Frank Den Oudsten, Philippe Van Cappellen, and Hendrikus J. Laanbroek. "Distribution and Diversity ofGallionella-Like Neutrophilic Iron Oxidizers in a Tidal Freshwater Marsh." Applied and Environmental Microbiology 77, no. 7 (February 11, 2011): 2337–44. http://dx.doi.org/10.1128/aem.02448-10.
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ABSTRACTMicrobial iron oxidation is an integral part of the iron redox cycle in wetlands. Nonetheless, relatively little is known about the composition and ecology of iron-oxidizing communities in the soils and sediments of wetlands. In this study, sediment cores were collected across a freshwater tidal marsh in order to characterize the iron-oxidizing bacteria (FeOB) and to link their distributions to the geochemical properties of the sediments. We applied recently designed 16S rRNA primers targetingGallionella-related FeOB by using a nested PCR-denaturing gradient gel electrophoresis (DGGE) approach combined with a novel quantitative PCR (qPCR) assay.Gallionella-related FeOB were detected in most of the samples. The diversity and abundance of the putative FeOB were generally higher in the upper 5 to 12 cm of sediment than in deeper sediment and higher in samples collected in April than in those collected in July and October. Oxygen supply by macrofauna appears to be a major force in controlling the spatial and temporal variations in FeOB communities. The higher abundance ofGallionella-related FeOB in April coincided with elevated concentrations of extractable Fe(III) in the sediments. Despite this coincidence, the distributions of FeOB did not exhibit a simple relationship to the redox zonation inferred from the geochemical depth profiles.
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Carter, Burchard D. "Inferring substrate preferences from test morphology in echinoids, and interpreting spatial and temporal patterns of diversity." Paleontological Society Papers 3 (October 1997): 121–45. http://dx.doi.org/10.1017/s1089332600000231.
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Preservational style of fossil echinoid tests allows assessment of the likelihood of post-mortem transport out of the preferred sediment type of the living echinoid. Sedimentologic study of the matrix of untransported specimens allows a check on functional morphologic inferences of the species' preferred sediment types. Functional morphologic analysis allows inference of a species preferred sediment type because the petals, fasciolaes, tubercles, ambulacral pores, ambulacral shape, and test profile control the echinoid's ability to burrow, and the grain size of sediment into which it is capable of doing so. Past studies have achieved better than 90% accuracy in predicting the grain size of thin sections of rocks containing echinoids, simply by interpretation of their functional morphology. Most mistaken predictions are attributable to species living in sediments that are less difficult to burrow in (sands) than those to which they are adapted (muds). Other species may live in sediments in which they are not well adapted by assuming an epifaunal mode of life.Relative proportions of species in an echinoid fauna preferring various sediment grain sizes, plotted for each of a number of localities, has proven useful in inferring generalized facies patterns within regions.Plots of temporal changes in echinoid species diversity through time correspond well to changes in proportions of species inferred to have preferred various substrate conditions, suggesting an environmental and taphonomic component to simple diversity curves.
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Ma, Yantian, Fangpeng Liu, Zhaoyu Kong, Jianhua Yin, Wenbo Kou, Lan Wu, and Gang Ge. "The Distribution Pattern of Sediment Archaea Community of the Poyang Lake, the Largest Freshwater Lake in China." Archaea 2016 (2016): 1–12. http://dx.doi.org/10.1155/2016/9278929.
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Archaea plays an important role in the global geobiochemical circulation of various environments. However, much less is known about the ecological role of archaea in freshwater lake sediments. Thus, investigating the structure and diversity of archaea community is vital to understand the metabolic processes in freshwater lake ecosystems. In this study, sediment physicochemical properties were combined with the results from 16S rRNA clone library-sequencing to examine the sediment archaea diversity and the environmental factors driving the sediment archaea community structures. Seven sites were chosen from Poyang Lake, including two sites from the main lake body and five sites from the inflow river estuaries. Our results revealed high diverse archaea community in the sediment of Poyang Lake, including Bathyarchaeota (45.5%), Euryarchaeota (43.1%), Woesearchaeota (3.6%), Pacearchaeota (1.7%), Thaumarchaeota (1.4%), suspended Lokiarchaeota (0.7%), Aigarchaeota (0.2%), and Unclassified Archaea (3.8%). The archaea community compositions differed among sites, and sediment property had considerable influence on archaea community structures and distribution, especially total organic carbon (TOC) and metal lead (Pb) (p<0.05). This study provides primary profile of sediment archaea distribution in freshwater lakes and helps to deepen our understanding of lake sediment microbes.
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Rodríguez-Martínez, Raquel, Guy Leonard, David S. Milner, Sebastian Sudek, Mike Conway, Karen Moore, Theresa Hudson, et al. "Controlled sampling of ribosomally active protistan diversity in sediment-surface layers identifies putative players in the marine carbon sink." ISME Journal 14, no. 4 (January 9, 2020): 984–98. http://dx.doi.org/10.1038/s41396-019-0581-y.
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AbstractMarine sediments are one of the largest carbon reservoir on Earth, yet the microbial communities, especially the eukaryotes, that drive these ecosystems are poorly characterised. Here, we report implementation of a sampling system that enables injection of reagents into sediments at depth, allowing for preservation of RNA in situ. Using the RNA templates recovered, we investigate the ‘ribosomally active’ eukaryotic diversity present in sediments close to the water/sediment interface. We demonstrate that in situ preservation leads to recovery of a significantly altered community profile. Using SSU rRNA amplicon sequencing, we investigated the community structure in these environments, demonstrating a wide diversity and high relative abundance of stramenopiles and alveolates, specifically: Bacillariophyta (diatoms), labyrinthulomycetes and ciliates. The identification of abundant diatom rRNA molecules is consistent with microscopy-based studies, but demonstrates that these algae can also be exported to the sediment as active cells as opposed to dead forms. We also observe many groups that include, or branch close to, osmotrophic–saprotrophic protists (e.g. labyrinthulomycetes and Pseudofungi), microbes likely to be important for detrital decomposition. The sequence data also included a diversity of abundant amplicon-types that branch close to the Fonticula slime moulds. Taken together, our data identifies additional roles for eukaryotic microbes in the marine carbon cycle; where putative osmotrophic–saprotrophic protists represent a significant active microbial-constituent of the upper sediment layer.
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Nold, Stephen C., Jizhong Zhou, Allan H. Devol, and James M. Tiedje. "Pacific Northwest Marine Sediments Contain Ammonia-Oxidizing Bacteria in the β Subdivision of theProteobacteria." Applied and Environmental Microbiology 66, no. 10 (October 1, 2000): 4532–35. http://dx.doi.org/10.1128/aem.66.10.4532-4535.2000.
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ABSTRACT The diversity of ammonia-oxidizing bacteria in aquatic sediments was studied by retrieving ammonia monooxygenase and methane monooxygenase gene sequences. Methanotrophs dominated freshwater sediments, while β-proteobacterial ammonia oxidizers dominated marine sediments. These results suggest that γ-proteobacteria such asNitrosococcus oceani are minor members of marine sediment ammonia-oxidizing communities.
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Dianto, Aan, Taofik Jasalesmana, Luki Subehi, Ahmad Yusuf Afandi, and Ardo Ramdhani. "Surface Sediment Diatom as A Water Quality Indicator: Case Study: Cilalay and Cibuntu Ponds, Cibinong." Indonesian Journal of Limnology 1, no. 1 (February 3, 2021): 38–46. http://dx.doi.org/10.51264/inajl.v1i1.1.
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Diatom is classified as algae within the Division of Bacillariophyta. They are unicellular eukaryotic organisms characterized by siliceous cell walls that can be long preserved in sediments. Therefore, diatom analysis in sediment records is a potential water quality indicator for present or paleo studies. The current knowledge on the distribution and diversity of diatoms in the sediment in the urban pond is poorly known. This study aimed to identify the distribution and diversity of diatoms from the sediments of the pond. We expect to obtain a primary database of a variety of diatoms. The sediment samples were taken from Cibuntu and Cilalay Ponds in Cibinong Botanical Garden. Sediments were digested using HCL and H2O2. The resulting diatom solution was dried and transferred onto glass coverslip, which subsequently mounted onto microscope slides using Naphrax (Refraction index 1.7). Diatom identification was examined using a light microscope at 1,000x magnification. Diatom communities in Cibuntu Pond were dominated by species Aulacoseria ambigua, Eunotia bilunaris, Cymbopleura sp, Discostella stelligera, and Rossithidium sp with diversity index of 2.4 and species evenness of 0.8. Whereas, species Fragilaria sp, Eunotia monodon, Navicymbula pusilla, Eunotia bilunaris, and Pinnularia viridis were predominant in Cilalay Pond with diversity index of 1.6 and species evenness of 0.5. Based on the diatom community, Cibuntu Pond is eutrophic indicated by the occurrence of Aulacoseria ambigua, whereas Cilalay Pond is meso-eutrophic indicated by the dominance of Fragillaria. This exploratory survey provides the first inventory of diatom assemblage in Cibuntu and Cilalay Ponds for roughly inferring the environmental changes in a shallow lake ecosystem.
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Nugroho, Fajar, Neviaty P. Zamani, and Hawis Madduppa. "THE EFFECT OF ORGANIC SEDIMENT CONTENT ON CORAL DIVERSITY IN KARIMUNJAWA ISLAND, INDONESIA." Jurnal Ilmu dan Teknologi Kelautan Tropis 10, no. 1 (April 1, 2018): 79–86. http://dx.doi.org/10.29244/jitkt.v10i1.21665.
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Coral reef now are under threats due to sedimentation. Fatal effect of organic rich sediment, leading corals mortality. Therefore, the study was conducted to investigate effect of organic sediment content to the coral diversity in Karimunjawa Island, Central Java, Indonesia. Field data was conducted at 6 locations. Three sediment traps were deployed at each sites to measure organic sediment content. Twenty replicated quadrant transects were used to estimate coral density and coral diversity. Analysis of variance (ANOVA) was used to examine the differences of organic sediment content in each station. The linear regression was used to assess the relationship between organic sediment content and coral diversity. Our field result demonstrated that sediment content significantly different between sites with value range from 0.42 mg/800 ml - 1.32 mg/800 ml. Based on the Simson’s Diversity Index, the highest coral diversity found at Alang-alang as site with low sedimentation while the lowest coral diversity was found at Legon Lele as site with high sedimentation. The study shown significant negative correlation between organic sediment content and coral diversity with the coefficient of regression 0.68. This study convinces that disturbance on coral reefs might affect coral diversity in Karimunjawa Island, in addition to other factors such as the influence of human activities, natural disruption and climate change. Keywords: sedimentation, organic, coral, diversity, Karimunjawa
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Stelzer, Patricia Sarcinelli, Ana Carolina A. Mazzuco, Luiz Eduardo Gomes, João Martins, Sergio Netto, and Angelo F. Bernardino. "Taxonomic and functional diversity of benthic macrofauna associated with rhodolith beds in SE Brazil." PeerJ 9 (July 29, 2021): e11903. http://dx.doi.org/10.7717/peerj.11903.
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Rhodoliths are free-living and morphologically diverse marine calcareous algae commonly distributed over the continental shelf seafloor. They increase the seabed structural complexity and are of potential value as feeding and reproductive grounds for a myriad of marine fauna. The higher structural seabed complexity within rhodolith beds may also increase benthic diversity by creating microhabitats, but this relationship has been rarely explored within rhodolith beds worldwide. Here we compared benthic macrofaunal (>500 µm) structure on rhodolith beds (nodule epifauna) and within unconsolidated sediments (sediment infauna) under high and low-density beds to test whether rhodolith bed density and nodule morphology influenced macrofaunal assemblages. We observed that macrofaunal density on nodules (2538 ± 288.7 ind·m−2) was 15-fold higher when compared to sediments under those beds (166 ± 38.8 ind·m−2). Rhodolith bed density was positively related to macrofaunal density, composition, and functional diversity on the rhodoliths. Low-density beds (61 ± 27.1 nodules·m−2) with discoid-shape nodules were dominated by peracarid crustaceans whereas high-density beds (204 ± 18.7 nodules·m−2) with spheroidal nodules were dominated by Annelid polychaetes. The sediment macrofauna was also positively influenced by the density of rhodolith nodules, which increased sediment carbonate and organic quality (protein and lipids) under high-density beds. Macrofaunal functional diversity was generally higher on rhodoliths, with low similarity (low nestedness) and high taxa turnover between macrofaunal assemblages of rhodoliths and sediments. These findings indicate that rhodolith beds provide an unique habitat for benthic macrofaunal communities, with exclusive functional and taxonomic richness that are likely not typical in the unconsolidated sediment below these beds in SE Brazil. This study highlights the importance of protecting rhodolith beds from multiple sources of anthropogenic disturbance and exploration on continental shelves.
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Hölker, Franz, Christian Wurzbacher, Carsten Weißenborn, Michael T. Monaghan, Stephanie I. J. Holzhauer, and Katrin Premke. "Microbial diversity and community respiration in freshwater sediments influenced by artificial light at night." Philosophical Transactions of the Royal Society B: Biological Sciences 370, no. 1667 (May 5, 2015): 20140130. http://dx.doi.org/10.1098/rstb.2014.0130.
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An increasing proportion of the Earth's surface is illuminated at night. In aquatic ecosystems, artificial light at night (ALAN) may influence microbial communities living in the sediments. These communities are highly diverse and play an important role in the global carbon cycle. We combined field and laboratory experiments using sediments from an agricultural drainage system to examine how ALAN affects communities and alters carbon mineralization. Two identical light infrastructures were installed parallel to a drainage ditch before the start of the experiment. DNA metabarcoding indicated that both sediment communities were similar. After one was lit for five months (July–December 2012) we observed an increase in photoautotroph abundance (diatoms, Cyanobacteria ) in ALAN-exposed sediments. In laboratory incubations mimicking summer and winter (six weeks each), communities in sediments that were exposed to ALAN for 1 year (July 2012–June 2013) showed less overall seasonal change compared with ALAN-naive sediments. Nocturnal community respiration was reduced in ALAN-exposed sediments. In long-term exposed summer-sediments, we observed a shift from negative to positive net ecosystem production. Our results indicate ALAN may alter sediment microbial communities over time, with implications for ecosystem-level functions. It may thus have the potential to transform inland waters to nocturnal carbon sinks.
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Wafula, Matthews, Agnes W. Muthumbi, Virginia Wangondu, Charles Kihia, and Julius Okondo. "Nematodes as bio-indicators of physical disturbance of marine sediments following polychaete bait harvesting." Western Indian Ocean Journal of Marine Science 19, no. 2 (April 2, 2021): 117–30. http://dx.doi.org/10.4314/wiojms.v19i2.9.
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Sediment disturbance in marine environments is caused by activities including polychaete bait harvesting, trawling, dredging, sediment erosion and treading. These activities affect the benthic communities by changing the densities, community assemblage and diversity. The aim of this study was to evaluate the potential of nematodes as indicators of sediments disturbance following polychaete bait harvesting. The study was conducted in three sites experiencing different bait harvesting intensities in Mida Creek, Kenya. Sediment samples were collected from the mudflats during low tide, preserved in 5% formalin and transported to the laboratory for processing and identification of nematodes. The highly disturbed site recorded the lowest nematode genus richness while the less disturbed sites had the highest. Overall, the most abundant nematode genera in the non-disturbed (Dabaso) and less disturbed sites (Kirepwe) were selective deposit feeders (Spirinia and Terschellingia), while most disturbed sites (e.g. Mayonda) had predators/omnivores (Pheronus, Aporcelaimellus) and selected members of the genus Spirinia. The disturbed site was characterised by low nematode diversity (H’) and low dominance (D) while the non-disturbed and less disturbed sites had higher diversity and dominance. Clearly, nematode community assemblage, diversity and feeding guilds changed following disturbance to a low diversity that favoured higher proportions of predator/omnivore taxa.
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Hope, J. A., G. Coco, D. R. Parsons, and S. F. Thrush. "Microplastics interact with benthic biostabilization processes." Environmental Research Letters 16, no. 12 (December 1, 2021): 124058. http://dx.doi.org/10.1088/1748-9326/ac3bfd.
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Abstract Marine microplastics (MPs) accumulate in sediments but impacts on ecosystem functions are poorly understood. MPs interactions with stabilizing benthic flora/fauna or biostabilization processes, have not been fully investigated, yet this is critical for unraveling MPs effects on ecosystem-scale processes and functions. This is also vital for understanding feedback processes that may moderate the stock and flow of MPs as they are transported through estuaries. The relationships between sedimentary MPs, biota, environmental properties and sediment stability from field sediments, were examined using variance partitioning (VP) and correlation analyses. VP was used to identify common and unique contributions of different groups of variables (environmental, fauna and microplastic variables) to sediment stability. The influence of microplastic presence (fragment/fiber abundances and microplastic diversity) on sediment stability (defined using erosion thresholds and erosion rates) was demonstrated. Furthermore, MPs appeared to mediate the biostabilizing effects of environmental properties (including microorganisms) and fauna. Environmental properties and sediment stability could also explain the variation in MPs across sites suggesting biostabilizing properties may mediate the abundance, type and diversity of MPs that accumulate in the bed. The potential for MPs to influence biota and biostabilization processes and mediate microplastic resuspension dynamics within estuaries is discussed.
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Luo, Yan, Zuo Ming Xie, Yi Fang Zhou, and Yan Xin Wang. "Bacterial Diversity in the High Arsenic Groundwater Systems of Jianghan Plain and Datong Basin by 16S rDNA Clone Library." Advanced Materials Research 726-731 (August 2013): 35–38. http://dx.doi.org/10.4028/www.scientific.net/amr.726-731.35.
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To compare the difference bacterial diversity between Jianghan plain and Datong basin. The high arsenic sediment samples in this study were collected from different depths of borehole. The bacterial diversity in high arsenic aquifer sediments was studied by 16S rDNA clone library. The dominant bacterial community included Burkholderiales, Pseudomonadales, and Enterobacteriales in Jianghan plain, and Burkholderiales,Enterobacteriales and Actinomycetales in Datong basin.
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Huang, S., C. Chen, X. Yang, Q. Wu, and R. Zhang. "Distribution of typical denitrifying functional genes and diversity of the <i>nirS</i>-encoding bacterial community related to environmental characteristics of river sediments." Biogeosciences 8, no. 10 (October 31, 2011): 3041–51. http://dx.doi.org/10.5194/bg-8-3041-2011.
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Abstract. Denitrification in river sediments leads to nitrate removal from the aquatic system; therefore, it is necessary to understand functional diversity of denitrifier communities in the system. Sediment samples (0–25 cm depth) were collected from three typical locations along the Pearl River. The real-time PCR approach was used to measure the abundance of nitrate (narG), nitrite (nirS, nirK and nrfA), and nitrous oxide (nosZ) reductase genes from the sediment samples. Assemblages of nirS, nirK and nosZ indicated that complete denitrification occurred in sediment cores, with the greatest number of gene copies from 5–15 cm depth. Dissimilatory nitrate reduction appeared to be important below 15 cm depth, based on increasing gene copies of narG and nrfA with sediment depth. There was a close match (78–94 %) between the nirS sequences recovered from the Pearl River sediment and those detected in estuarine and marine sediments as well as active sludge, suggesting that the nitrogen source in the Pearl River sediment was affected by domestic sewage inputs and irregular tides. Canonical correspondence analysis indicated that the spatial distribution of denitrifying bacteria was highly correlated with dissolved inorganic nitrogen (including NH4+, NO2− and NO3−) concentrations in sediment. It was concluded that the difference in dissolved inorganic nitrogen concentrations along the sediment profile influenced the distribution of denitrifying genes and the nirS-encoding denitrifier community in the river sediment. In addition, a variety of novel denitrifying bacteria were revealed in the river sediment.
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Takarina, Noverita Dian, Ayu Maulida Sukma, Andrio Adiwibowo, and Sitaresmi Sitaresmi. "Water Quality and Microbial Community Assessment in Artisanal Mining- Affected Sediments of Cikidang River, Banten, Java, Indonesia." Sains Malaysiana 51, no. 5 (May 31, 2022): 1339–52. http://dx.doi.org/10.17576/jsm-2022-5105-06.
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The total microbial diversity and community in submerged sediments near mining sites, transition and intact sites at Cikidang River, Banten were assessed using 16S rDNA sequence data and biodiversity indices. Assessed water quality parameters in the river were water current, dissolved oxygen (DO), pH, redox potential, salinity, temperature and turbidity. Microbial alpha diversity used were Shannon diversity index, ChaoI index and Operational Taxonomic Units (OTUs). These analyses indicated a total of 50 taxa of sediment microbes. Based on Shannon diversity index, the highest value was observed at mining site. High abundant microbes in sediments at mining sites for phylum, class, order, family and genera levels were represented by Proteobacteria, Gammaproteobacteria, Pseudomonadales, Moraxellaceae, and Acinetobacter, respectively. In contrast, high abundant microbes in the sediment of the intact site for each taxon consisted of Firmicutes, Alphaproteobacteria, Erysipelotrichales, Erysipelotrichaceae, and Erysipelothrix. The water quality of mining sites was characterised by alkaline pH (8.807, 95% CI: 8.624 - 8.990) and lower redox potential (59.000 mV, 95% CI: 36.233 - 81.767) that differed significantly from the intact sites (P<0.05). This study also confirmed that mining sites have a higher genus diversity. Research on potential microbes of related genus as bioremediators could be recommended for further study.
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Bitenieks, Krišs, Arta Bārdule, Karin Eklöf, Mikk Espenberg, Dainis Edgars Ruņģis, Zane Kļaviņa, Ivars Kļaviņš, Haiyan Hu, and Zane Lībiete. "The Influence of the Degree of Forest Management on Methylmercury and the Composition of Microbial Communities in the Sediments of Boreal Drainage Ditches." Microorganisms 10, no. 10 (October 6, 2022): 1981. http://dx.doi.org/10.3390/microorganisms10101981.
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Inorganic mercury (Hg) can be methylated to the highly toxic and bioavailable methylmercury (MeHg) by microorganisms in anaerobic environments. The Hg methylation rate may be affected by forest management activities, which can influence the catchment soils, water, and sediments. Here, we investigate the influence of forest management in the form of ditch cleaning and beaver dam removal, as well as the seasonal variations, on sediment chemistry and microbiota. The relationships between MeHg concentrations in sediment samples and archaeal and bacterial communities assessed by 16S rRNA gene amplicon sequencing were investigated to determine the microbial conditions that facilitated the formation of MeHg. Concentrations of MeHg were highest in undisturbed catchments compared to disturbed or slightly disturbed sites. The undisturbed sites also had the highest microbial diversity, which may have facilitated the formation of MeHg. Low MeHg concentrations and microbial diversity were observed in disturbed sites, which may be due to the removal of organic sediment layers during ditch cleaning and beaver dam removal, resulting in more homogenous, mineral-rich environments with less microbial activity. MeHg concentrations were higher in summer and autumn compared to winter and spring, but the temporal variation in the composition and diversity of the microbial community was less than the spatial variation between sites. Beta diversity was more affected by the environment than alpha diversity. The MeHg concentrations in the sediment were positively correlated to several taxa, including Cyanobacteria, Proteobacteria, Desulfobacterota, Chloroflexi, and Bacteroidota, which could represent either Hg-methylating microbes or the growth substrates of Hg-methylating microbes.
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Suryono, Chrisna Adhi. "Akumulasi Logam Berat Cr, Pb dan Cu dalam Sedimen dan Hubungannya dengan Organisme Dasar di Perairan Tugu Semarang." Jurnal Kelautan Tropis 19, no. 2 (December 5, 2016): 143. http://dx.doi.org/10.14710/jkt.v19i2.841.
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The concentrations of metals in the marine sediment were found in coatal areas of Tugu Semarang. Three metals (Cr, Pb and, Cu) has found in coastal areas in research area. Shingly significantly those heavy metals have significantly influences on the abundance and diversity of benthic organisms. That has been proved by regression test which number of r= 0,99 on abundance and r= 0,92 on diversity. The increasing of heavy metals concentration will following of the number of abundance and diversity of benthic organisms in that area. Keywords: Metals, sediment,benthick organisms Konsentrasi logam berat telah ditemukan dalam sedimen laut ut di daerah pesisir Tugu Semarang. Tiga logam berat seperti (Cr, Pb, dan Cu) telah ditemukan di lokasi penelitian. Secara nyata terlihat bahwa logam tersebut berpengaruh terhadap kelimpahan dan keanekaragaman organisme dasar perairan. Hal tersebut dibuktikan dengan regresi berganda antara kelimpahan organisme dengan logam berat dalam sedimen dengan nilai r = 0,99, sedangkan hubungan antara keanekaragaman dengan dengan logam berat dalam sediemen dengan nilai r = 0,92. Peningkatan konsentrasi logam berat dalam sediiemen akan diikuti penurunan kelimpahan dan keanekaragaman organisme dasar perairan. Kata Kunci: Logam berat, sedimen, organisme dasar
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Lestari, Arini Indah, Mustofa Niti Supardjo, and Boedi Hendrarto. "HUBUNGAN ANTARA SEDIMEN DENGAN LOGAM BERAT DAN MAKROZOOBENTOS DI SUNGAI SIANGKER, SEMARANG." Management of Aquatic Resources Journal (MAQUARES) 5, no. 4 (December 20, 2016): 337–44. http://dx.doi.org/10.14710/marj.v5i4.14439.
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ABSTRAK Sungai Siangker merupakan salah satu sub sistem dari sistem drainase Semarang Barat yang mengalami pendangkalan.Limbah yang berasal dari pabrik diduga mengandung logam berat Pb dan Cd. Oleh karena itu, penelitian ini diadakan untuk mengetahui kadar logam berat Pb dan Cd dan hubungan antara sedimen serta kandungan logam berat Pb dan Cd dengan komunitas makrozoobentos. Pengambilan sampel dilakukan secara random sampling. PCA (Principle Component Analysis) digunakan untuk mengetahui kedekatan hubungan antara makrozoobentos, nilai bahan organik dan karakteristik sedimen.Perbedaan variabel tiap stasiunnya diuji dengan Uji Kruskal-Wallis. Korelasi Pearson digunakan untuk menganalisis hubungan antara variabel kelimpahan, keanekaragaman, kadar logam berat dan karakteristik sedimen di tiap stasiunnya. Hasil rerata yang diperoleh dari analisa kadar logam berat (Pb) di muara dan sungai Siangker adalah 1,10 – 1,64 mg/l, sedangkan untuk rerata (Cd) sebesar 0,13 – 0,43 mg/l. Kadar debu mempunyai korelasi positif yang erat (p < 0,05) dengan keanekaragaman dan kelimpahan makrozoobentos. Kadar logam berat berpengaruh nyata (p < 0,05) terhadap keanekaragaman maupun kelimpahan makrozoobentos. Kata Kunci : Sungai, logam berat, karakteristik sedimen, makrozoobentos ABSTRACTSiangker river is one of the sub-systems of the West Semarang drainage system that experiencing siltation. Waste from the factories is suspected to contain heavy metals (Pb) and (Cd). This study was conducted to understand concentration of Pb and Cd and the relationship between characteristics of the sediments containing heavy metals (Pb) and (Cd) as well as macrozoobenthos community. Sampling was done by random sampling. PCA (Principle Component Analysis) was used to determine proximity of the relationships between macrozoobenthos and the value of organic matter as well as sediment characteristics. Meanwhile, the differences in the station of each variable was tested using Kruskal-Wallis test. Pearson correlation was used to analyze the relationship between abundance variables, diversity, the levels of heavy metals and sediment characteristics in each station. The results showed that the levels of heavy metals (Pb) in the estuary and river Siangker were 1,10 to 1,64 mg / l, while concentration of (Cd) is 0,13 to 0,43 mg / l. Dust levels were closely positively correlated (p < 0,05) with the diversity and abundance of macrozoobenthos. Levels of heavy metals was significant (p < 0,05) for the diversity and abundance of macrozoobenthos. Keywords : River, heavy metal, sediment characteristic, macrozoobenthos
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Sauer, Hailey M., Trinity L. Hamilton, Rika E. Anderson, Charles E. Umbanhowar, and Adam J. Heathcote. "Diversity and distribution of sediment bacteria across an ecological and trophic gradient." PLOS ONE 17, no. 3 (March 21, 2022): e0258079. http://dx.doi.org/10.1371/journal.pone.0258079.
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The microbial communities of lake sediments have the potential to serve as valuable bioindicators and integrators of watershed land-use and water quality; however, the relative sensitivity of these communities to physio-chemical and geographical parameters must be demonstrated at taxonomic resolutions that are feasible by current sequencing and bioinformatic approaches. The geologically diverse and lake-rich state of Minnesota (USA) is uniquely situated to address this potential because of its variability in ecological region, lake type, and watershed land-use. In this study, we selected twenty lakes with varying physio-chemical properties across four ecological regions of Minnesota. Our objectives were to (i) evaluate the diversity and composition of the bacterial community at the sediment-water interface and (ii) determine how lake location and watershed land-use impact aqueous chemistry and influence bacterial community structure. Our 16S rRNA amplicon data from lake sediment cores, at two depth intervals, data indicate that sediment communities are more likely to cluster by ecological region rather than any individual lake properties (e.g., trophic status, total phosphorous concentration, lake depth). However, composition is tied to a given lake, wherein samples from the same core were more alike than samples collected at similar depths across lakes. Our results illustrate the diversity within lake sediment microbial communities and provide insight into relationships between taxonomy, physicochemical, and geographic properties of north temperate lakes.
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Rachman, Arief, Hikmah Thoha, Mariana Destila Bayu Intan, Oksto Ridho Sianturi, Yunia Witasari, Singgih Prasetyo Adi Wibowo, and Mitsunori Iwataki. "Dinoflagellate Cyst Distribution in Relation to the Sediment Composition and Grain Size in the Coastal Area of Pangkajene, South Sulawesi, Indonesia." ILMU KELAUTAN: Indonesian Journal of Marine Sciences 27, no. 2 (April 13, 2022): 111–23. http://dx.doi.org/10.14710/ik.ijms.27.2.111-123.
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Dinoflagellate cysts have an important role for their bloom dynamics, which are commonly deposited along fine sediment grains and become the source of the next bloom. This study aimed to describe the cyst banks species composition, and their relationship with the sediment particles size and plankton composition in the coast of Pangkajene, South Sulawesi. Cysts observed in this study were extracted from seabed sediments collected from 9 sites. A potential cyst bank, with a cyst density of 240 cysts.g-1 sediment wet weight was found at PK-19, located in proximity to a large harbour complex. Although unusual, cyst density was significantly and positively correlated with the percentage of gravel. In contrast, the diversity of cysts seems to be affected by the percentage of fine sediments, such as silt and clay. None of the sediment composition was found strongly and significantly affecting both cyst density and diversity. A southward increase in cyst density was similar to the trend in the cell density of its planktonic form. Cysts of Protoperidinium spp., Scrippsiella spp., and Pheopolykrikos hartmannii were common and abundant in the sediment. Aside from Protoperidinium spp., most dinoflagellate species found in cyst form were absent from the water column. The occurrence of cysts of harmful dinoflagellates with records of devastating blooms in other coastal areas in Indonesia, such as Margalefidinium polykrikoides, Pyrodinium bahamense, and Gymnodinium catenatum, signifies a need to regularly monitor the area around Pangkajene coast to mitigate impacts of future blooms.
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Ozbayram, E. Gozde, Latife Köker, Ayça Oğuz Çam, Reyhan Akçaalan, and Meriç Albay. "Temporal and Spatial Variations of the Bacterial Diversity in a Deep Alkaline Lake." Water 14, no. 24 (December 15, 2022): 4097. http://dx.doi.org/10.3390/w14244097.
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This study aimed to investigate the effects of thermal stratification and complete mixing conditions on the bacterial diversity of a deep alkaline lake. For this purpose, the water and sediment samples were collected during the winter turnover and stratification periods, and bacterial communities were assessed by metabarcoding. The results showed that temperature shaped the bacterial community patterns in the lake. While the bacterial communities of the water samples showed high similarity during the mixing period, communities had distinctive patterns in the epilimnion and hypolimnion during stratification. The diversity and evenness of the bacterial communities increased with depth, whereas the bacterial communities of sediments were more even and diverse than in water. Proteobacteria members dominated the sediment communities representing 41% to 62% of the total reads in the samples. Particularly, Gammaproteobacteria was the major class found in the sediment; higher abundances were recorded in the mixing period representing 33–51%. Additionally, Actinobacteria species were more abundant in the water samples representing 22–52% of all reads during the stratification period. Due to the complete mixing conditions in the lake, a homogenized bacterial community structure was observed in the lake with minor spatial changes, and a clear divergence was observed between epilimnion and hypolimnion. On the other hand, the sediment bacterial community showed a more stable profile.
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Yasir, Muhammad, Arooj K. Qureshi, and Esam I. Azhar. "16S amplicon sequencing of microbial communities in enriched and non-enriched sediments of non-volcanic hot spring with temperature gradients." PeerJ 9 (April 2, 2021): e10995. http://dx.doi.org/10.7717/peerj.10995.
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Microorganisms in geothermal springs can offer insights into the fundamental and applied study of extremophiles. However, low microbial abundance and culturing requirements limit the ability to analyze microbial diversity in these ecosystems. In this study, culture-dependent and culture-independent techniques were used to analyze sediment samples from the non-volcanic Tatta Pani hot springs in district Poonch of Azad Kashmir. Microbial composition, temperature gradient, and enrichment effects on rare taxa were evaluated. In total, 31 distinct bacterial phyla and 725 genera were identified from the non-enriched Tatta Pani hot spring sediment samples, and 33 distinct bacterial phyla and 890 genera from the enriched sediment samples. Unique phyla specimens from the enriched samples included Candidatus Cloacimonetes, Caldiserica, and Korarchaeota archaea. The enriched samples yielded specific microbiota including 805 bacteria and 42 archaea operational taxonomic units with 97% similarity, though decreased thermophilic microbiota were observed in the enriched samples. Microbial diversity increased as temperature decreased. Candidate novel species were isolated from the culture-dependent screening, along with several genera that were not found in the 16S amplicon sequencing data. Overall, the enriched sediments showed high microbial diversity but with adverse changes in the composition of relatively dominant bacteria. Metagenomic analyses are needed to study the diversity, phylogeny, and functional investigation of hot spring microbiota.
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Newell, Silvia E., Kaitlyn R. Pritchard, Sarah Q. Foster, and Robinson W. Fulweiler. "Molecular evidence for sediment nitrogen fixation in a temperate New England estuary." PeerJ 4 (January 25, 2016): e1615. http://dx.doi.org/10.7717/peerj.1615.
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Primary production in coastal waters is generally nitrogen (N) limited with denitrification outpacing nitrogen fixation (N2-fixation). However, recent work suggests that we have potentially underestimated the importance of heterotrophic sediment N2-fixation in marine ecosystems. We used clone libraries to examine transcript diversity ofnifH(a gene associated with N2-fixation) in sediments at three sites in a temperate New England estuary (Waquoit Bay, Massachusetts, USA) and compared our results to net sediment N2fluxes previously measured at these sites. We observednifHexpression at all sites, including a site heavily impacted by anthropogenic N. At this N impacted site, we also observed mean net sediment N2-fixation, linking the geochemical rate measurement withnifHexpression. This same site also had the lowest diversity (non-parametric Shannon = 2.75). At the two other sites, we also detectednifHtranscripts, however, the mean N2flux indicated net denitrification. These results suggest that N2-fixation and denitrification co-occur in these sediments. Of the unique sequences in this study, 67% were most closely related to uncultured bacteria from various marine environments, 17% to Cluster III, 15% to Cluster I, and only 1% to Cluster II. These data add to the growing body of literature that sediment heterotrophic N2-fixation, even under high inorganic nitrogen concentrations, may be an important yet overlooked source of N in coastal systems.
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Dang, Hongyue, Ruipeng Chen, Lin Wang, Lizhong Guo, Pingping Chen, Zuwang Tang, Fang Tian, Shaozheng Li, and Martin G. Klotz. "Environmental Factors Shape Sediment Anammox Bacterial Communities in Hypernutrified Jiaozhou Bay, China." Applied and Environmental Microbiology 76, no. 21 (September 10, 2010): 7036–47. http://dx.doi.org/10.1128/aem.01264-10.
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ABSTRACT Bacterial anaerobic ammonium oxidation (anammox) is an important process in the marine nitrogen cycle. Because ongoing eutrophication of coastal bays contributes significantly to the formation of low-oxygen zones, monitoring of the anammox bacterial community offers a unique opportunity for assessment of anthropogenic perturbations in these environments. The current study used targeting of 16S rRNA and hzo genes to characterize the composition and structure of the anammox bacterial community in the sediments of the eutrophic Jiaozhou Bay, thereby unraveling their diversity, abundance, and distribution. Abundance and distribution of hzo genes revealed a greater taxonomic diversity in Jiaozhou Bay, including several novel clades of anammox bacteria. In contrast, the targeting of 16S rRNA genes verified the presence of only “Candidatus Scalindua,” albeit with a high microdiversity. The genus “Ca. Scalindua” comprised the apparent majority of active sediment anammox bacteria. Multivariate statistical analyses indicated a heterogeneous distribution of the anammox bacterial assemblages in Jiaozhou Bay. Of all environmental parameters investigated, sediment organic C/organic N (OrgC/OrgN), nitrite concentration, and sediment median grain size were found to impact the composition, structure, and distribution of the sediment anammox bacterial community. Analysis of Pearson correlations between environmental factors and abundance of 16S rRNA and hzo genes as determined by fluorescent real-time PCR suggests that the local nitrite concentration is the key regulator of the abundance of anammox bacteria in Jiaozhou Bay sediments.
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Huang, S., C. Chen, Q. Wu, R. Zhang, and X. Yang. "Distribution of typical denitrifying functional genes and diversity of the <i>nirS</i>-encoding bacterial community related to environmental characteristics of river sediments." Biogeosciences Discussions 8, no. 3 (May 31, 2011): 5251–80. http://dx.doi.org/10.5194/bgd-8-5251-2011.
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Abstract. Denitrification in river sediments leads to nitrate removal from the aquatic system; therefore, it is necessary to understand functional diversity of denitrifier communities in the system. Sediment samples (0–25 cm depth) were collected from three typical locations along the Pearl River. The real-time PCR approach was used to measure the abundance of nitrate (narG), nitrite (nirS, nirK and nrfA), and nitrous oxide (nosZ) reductase genes from the sediment samples. Assemblages of nirS, nirK and nosZ indicated that complete denitrification occurred in sediment cores, with the greatest number of gene copies from 5–15 cm depth. Dissimilatory nitrate reduction appeared to be important below 15 cm depth, based on increasing gene copies of narG and nrfA with sediment depth. There was a close match (78–94 %) between the nirS sequences recovered from Pearl River sediment and those detected in estuarine and marine sediments as well as active sludge, suggesting that domestic sewage inputs and irregular tides. Canonical correspondence analysis indicated that the spatial distribution of denitrifying bacteria was highly correlated with dissolved inorganic N (DIN: NH4+, NO2
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MOHD ISMAILLUDDIN, SITI AMINAH, MAIZAH MOHD ABDULLAH, YUSOF SHUAIB IBRAHIM, and IZWANDY IDRIS. "BENTHIC COMMUNITY DIVERSITY AT MARINE ARCHAEOLOGICAL SITE, PULAU BIDONG, SOUTH CHINA SEA." Universiti Malaysia Terengganu Journal of Undergraduate Research 3, no. 3 (July 31, 2021): 93–106. http://dx.doi.org/10.46754/umtjur.v3i3.222.
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An artificial structure on the seafloor will affect the structure of the benthic community. This structure may include a sunken ship or a century-old building that becomes an underwater heritage site. Benthic communities at underwater archaeological sites have been studied around the world, though it is lacking in Malaysia. This study aimed to determine the benthic community composition and diversity in sediment and on an artifact (small ceramic pot) at the marine “Bidong shipwreck” archaeological site. SCUBA divers collected samples (sediment and artifact) from an 18 m depth archaeological site in October 2017. Then, all samples were fixed with 10% buffered formalin and preserved in 80% ethanol prior to identification analysis. Most benthic organisms were identified until class taxon, except for class Polychaeta until family. A total of 2711 benthic organisms which belonged to eight phyla, and 17 classes were recorded, of which 638 are polychaetes. In the archaeological site, Syllidae was the most abundant family in the sediment, and the family Nereididae dominated in artifact while Capitellidae was dominant at the control site. Shannon-Weiner diversity index showed variation and ranged from 1.5 to 2.1, while the evenness index value ranged from 0.56 to 0.77. The benthic community in sediment on both sites were more diverse and even compared to the artifact. Simultaneously, Jaccard’s similarity test discovered that the benthic community’s composition in sediment at the control site was highly similar to the archaeological site (0.80) comparatively to the artifact (0.65). It is suggested that the benthic community at the archaeological site has reached an equilibrium state similar to the control site. The scouring process may influence the lower benthic community composition on the artifact than sediments in its surroundings. These findings provide an overview of benthic community’s post-disturbance resilience and reveal a marine archaeological site’s ecological status.
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Zhang, Zhimin, Qinghui Deng, Lingling Wan, Xiuyun Cao, Yiyong Zhou, and Chunlei Song. "Bacterial Communities and Enzymatic Activities in Sediments of Long-Term Fish and Crab Aquaculture Ponds." Microorganisms 9, no. 3 (February 26, 2021): 501. http://dx.doi.org/10.3390/microorganisms9030501.
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Aquaculture is among the most important and fastest growing agriculture sectors worldwide; however, it generates environmental impacts by introducing nutrient accumulations in ponds, which are possibly different and further result in complex biological processes in the sediments based on diverse farming practices. In this study, we investigated the effects of long-term farming practices of representative aquatic animals dominated by grass carp (GC, Ctenopharyngodon idella) or Chinese mitten crab (CMC, Eriocheir sinensis) on the bacterial community and enzyme activity of sediments from more than 15 years of aquaculture ponds, and the differences associated with sediment properties were explored in the two farming practices. Compared to CMC ponds, GC ponds had lower contents of TC, TN, and TP in sediments, and similar trends for sediment pH and moisture content. Sediment bacterial communities were significantly different between GC and CMC ponds, with higher bacterial richness and diversity in GC ponds. The bacterial communities among the pond sediments were closely associated with sediment pH, TC, and TN. Additionally, the results showed profoundly lower activities of β-1,4-glucosidase, leucine aminopeptidase, and phosphatase in the sediments of GC ponds than CMC ponds. Pearson’s correlation analysis further revealed strong positive correlations between the hydrolytic enzyme activities and nutrient concentrations among the aquaculture ponds, indicating microbial enzyme regulation response to sediment nutrient dynamics. Our study herein reveals that farming practices of fish and crab differently affect bacterial communities and enzymatic activities in pond sediments, suggesting nutrient-driven sediment biological processes in aquaculture ponds for different farming practices.
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Doherty, Mary, Maiko Tamura, Jan A. C. Vriezen, George B. McManus, and Laura A. Katz. "Diversity of Oligotrichia and Choreotrichia Ciliates in Coastal Marine Sediments and in Overlying Plankton." Applied and Environmental Microbiology 76, no. 12 (April 30, 2010): 3924–35. http://dx.doi.org/10.1128/aem.01604-09.
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ABSTRACT Elucidating the relationship between ciliate communities in the benthos and the plankton is critical to understanding ciliate diversity in marine systems. Although data for many lineages are sparse, at least some members of the dominant marine ciliate clades Oligotrichia and Choreotrichia can be found in both plankton and benthos, in the latter either as cysts or active forms. In this study, we developed a molecular approach to address the relationship between the diversity of ciliates in the plankton and those of the underlying benthos in the same locations. Samples from plankton and sediments were compared across three sites along the New England coast, and additional subsamples were analyzed to assess reproducibility of methods. We found that sediment and plankton subsamples differed in their robustness to repeated subsampling. Sediment subsamples (i.e., 1-g aliquots from a single ∼20-g sample) gave variable estimates of diversity, while plankton subsamples produced consistent results. These results indicate the need for additional study to determine the spatial scale over which diversity varies in marine sediments. Clustering of phylogenetic types indicates that benthic assemblages of oligotrichs and choreotrichs appear to be more like those from spatially remote benthic communities than the ciliate communities sampled in the water above them.