Relevant bibliographies by topics / Sediment microbial communities

Academic literature on the topic 'Sediment microbial communities'

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Published: 10 March 2023

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Journal articles on the topic "Sediment microbial communities"

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Li, Junwei, Suwen Chen, Peng Wu, Changbo Zhu, Ruiping Hu, Ting Li, and Yongjian Guo. "Insights into the Relationship between Intestinal Microbiota of the Aquaculture Worm Sipunculus nudus and Surrounding Sediments." Fishes 8, no. 1 (January 3, 2023): 32. http://dx.doi.org/10.3390/fishes8010032.

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Sipunculus nudus is an important intertidal aquaculture species that can ingest organic matter from the surface sediment and shows a high transportation capacity in sediment. However, little is known about the influence of intertidal aquaculture species on the sediment microbial community and the exchange of microbiota between the intestine and the surrounding sediment. In this study, the microbial communities in the intestine of S. nudus and three kinds of surrounding sediments were analyzed using high-throughput sequencing of the 16S rRNA gene amplicon, and the relationships between different communities were examined. Principal coordinate analysis and ANOSIM/Adonis analysis showed that the microbial communities of worm intestine samples were significantly different from those of surrounding sediments (p < 0.05). Meanwhile, compared with the sediment samples, the microbial α-diversity was significantly lower in the intestinal samples. Although the relative abundances of Proteobacteria and Cyanobacteria were high in all samples, three phyla (Bacteroidetes, Gemmatimonadetes, and Latescibacteria) showed a great difference between the four groups, as the abundances of the three phyla were significantly lower in the intestinal samples. Moreover, several microbial interactions were found between the worm intestine and surrounding sediments. BugBase functional prediction analysis indicated that the oxygen status of the sediment and the intestine was changed by bioturbation by the worm. Therefore, the microenvironment and microbial community in sediment were affected by the activity of S. nudus in the intertidal aquaculture zone.
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Oest, Adam, Ali Alsaffar, Mitchell Fenner, Dominic Azzopardi, and Sonia M. Tiquia-Arashiro. "Patterns of Change in Metabolic Capabilities of Sediment Microbial Communities in River and Lake Ecosystems." International Journal of Microbiology 2018 (May 27, 2018): 1–15. http://dx.doi.org/10.1155/2018/6234931.

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Information on the biodegradation potential of lake and river microbial communities is essential for watershed management. The water draining into the lake ecosystems often carries a significant amount of suspended sediments, which are transported by rivers and streams from the local drainage basin. The organic carbon processing in the sediments is executed by heterotrophic microbial communities, whose activities may vary spatially and temporally. Thus, to capture and apprehend some of these variabilities in the sediments, we sampled six sites: three from the Saint Clair River (SC1, SC2, and SC3) and three from Lake Saint Clair in the spring, summer, fall, and winter of 2016. Here, we investigated the shifts in metabolic profiles of sediment microbial communities, along Saint Clair River and Lake Saint Clair using Biolog EcoPlates, which test for the oxidation of 31 carbon sources. The number of utilized substrates was generally higher in the river sediments (upstream) than in the lake sediments (downstream), suggesting a shift in metabolic activities among microbial assemblages. Seasonal and site-specific differences were also found in the numbers of utilized substrates, which were similar in the summer and fall, and spring and winter. The sediment microbial communities in the summer and fall showed more versatile substrate utilization patterns than spring and winter communities. The functional fingerprint analyses clearly distinguish the sediment microbial communities from the lake sites (downstream more polluted sites), which showed a potential capacity to use more complex carbon substrates such as polymers. This study establishes a close linkage between physical and chemical properties (temperature and organic matter content) of lake and river sediments and associated microbial functional activities.
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Rutere, Cyrus, Kirsten Knoop, Malte Posselt, Adrian Ho, and Marcus A. Horn. "Ibuprofen Degradation and Associated Bacterial Communities in Hyporheic Zone Sediments." Microorganisms 8, no. 8 (August 16, 2020): 1245. http://dx.doi.org/10.3390/microorganisms8081245.

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Ibuprofen, a non-steroidal anti-inflammatory pain reliever, is among pharmaceutical residues of environmental concern ubiquitously detected in wastewater effluents and receiving rivers. Thus, ibuprofen removal potentials and associated bacteria in the hyporheic zone sediments of an impacted river were investigated. Microbially mediated ibuprofen degradation was determined in oxic sediment microcosms amended with ibuprofen (5, 40, 200, and 400 µM), or ibuprofen and acetate, relative to an un-amended control. Ibuprofen was removed by the original sediment microbial community as well as in ibuprofen-enrichments obtained by re-feeding of ibuprofen. Here, 1-, 2-, 3-hydroxy- and carboxy-ibuprofen were the primary transformation products. Quantitative real-time PCR analysis revealed a significantly higher 16S rRNA abundance in ibuprofen-amended relative to un-amended incubations. Time-resolved microbial community dynamics evaluated by 16S rRNA gene and 16S rRNA analyses revealed many new ibuprofen responsive taxa of the Acidobacteria, Actinobacteria, Bacteroidetes, Gemmatimonadetes, Latescibacteria, and Proteobacteria. Two ibuprofen-degrading strains belonging to the genera Novosphingobium and Pseudomonas were isolated from the ibuprofen-enriched sediments, consuming 400 and 300 µM ibuprofen within three and eight days, respectively. The collective results indicated that the hyporheic zone sediments sustain an efficient biotic (micro-)pollutant degradation potential, and hitherto unknown microbial diversity associated with such (micro)pollutant removal.
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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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Wu, Miao, Ming Zhang, Wei Ding, Lin Lan, Zhilin Liu, Lingzhan Miao, and Jun Hou. "Microbial Carbon Metabolic Functions in Sediments Influenced by Resuspension Event." Water 13, no. 1 (December 23, 2020): 7. http://dx.doi.org/10.3390/w13010007.

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Microorganisms in sediments are an important part of the aquatic ecosystem, and their functional activities are sensitive to external environmental pressure. Shallow lakes are characterized by frequent sediment resuspension events, leading to large amounts of nutrients being released. However, information about the potential impacts of sediment resuspension events on the functional activities of microbial communities is limited. In this study, the responses of microbial carbon metabolism in sediments under different wind–wave disturbance were analyzed by BIOLOG ECO microplates. The results showed that under four disturbance conditions (wind speeds of 0, 1.60, 3.62, and 14.10 m/s), the total carbon metabolism function of the sediment microbial community (represented as average well-color development, AWCD) remained unchanged (p > 0.05), and the final total AWCD value stabilized at about 1.70. However, compared with the control group, some specific carbon sources (e.g., amines and carboxylic acids) showed significant changes (p < 0.05). We found that short-term (8 h) resuspension events did not affect the total carbon metabolism of sediment microbial communities, while it affected the microbial utilization ability of some specific types of carbon sources. For example, we found that the microbial utilization capacity of polymers in the 14.10 m/s group was the best. This study provides a new insight into the carbon cycle process of shallow lake sediments that resuspension events will affect the carbon cycle process of sediments.
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Kuo, Jimmy, Daniel Liu, and Chorng-Horng Lin. "Functional Prediction of Microbial Communities in Sediment Microbial Fuel Cells." Bioengineering 10, no. 2 (February 3, 2023): 199. http://dx.doi.org/10.3390/bioengineering10020199.

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Sediment microbial fuel cells (MFCs) were developed in which the complex substrates present in the sediment could be oxidized by microbes for electron production. In this study, the functional prediction of microbial communities of anode-associated soils in sediment MFCs was investigated based on 16S rRNA genes. Four computational approaches, including BugBase, Functional Annotation of Prokaryotic Taxa (FAPROTAX), the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2), and Tax4Fun2, were applied. A total of 67, 9, 37, and 38 functional features were statistically significant. Among these functional groups, the function related to the generation of precursor metabolites and energy was the only one included in all four computational methods, and the sum total of the proportion was 93.54%. The metabolism of cofactor, carrier, and vitamin biosynthesis was included in the three methods, and the sum total of the proportion was 29.94%. The results suggested that the microbial communities usually contribute to energy metabolism, or the metabolism of cofactor, carrier, and vitamin biosynthesis might reveal the functional status in the anode of sediment MFCs.
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Laverock, Bonnie, Jack A. Gilbert, Karen Tait, A. Mark Osborn, and Steve Widdicombe. "Bioturbation: impact on the marine nitrogen cycle." Biochemical Society Transactions 39, no. 1 (January 19, 2011): 315–20. http://dx.doi.org/10.1042/bst0390315.

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Sediments play a key role in the marine nitrogen cycle and can act either as a source or a sink of biologically available (fixed) nitrogen. This cycling is driven by a number of microbial remineralization reactions, many of which occur across the oxic/anoxic interface near the sediment surface. The presence and activity of large burrowing macrofauna (bioturbators) in the sediment can significantly affect these microbial processes by altering the physicochemical properties of the sediment. For example, the building and irrigation of burrows by bioturbators introduces fresh oxygenated water into deeper sediment layers and allows the exchange of solutes between the sediment and water column. Burrows can effectively extend the oxic/anoxic interface into deeper sediment layers, thus providing a unique environment for nitrogen-cycling microbial communities. Recent studies have shown that the abundance and diversity of micro-organisms can be far greater in burrow wall sediment than in the surrounding surface or subsurface sediment; meanwhile, bioturbated sediment supports higher rates of coupled nitrification–denitrification reactions and increased fluxes of ammonium to the water column. In the present paper we discuss the potential for bioturbation to significantly affect marine nitrogen cycling, as well as the molecular techniques used to study microbial nitrogen cycling communities and directions for future study.
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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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Marfil-Santana, Miguel David, Anahí Martínez-Cárdenas, Analuisa Ruíz-Hernández, Mario Vidal-Torres, Norma Angélica Márquez-Velázquez, Mario Figueroa, and Alejandra Prieto-Davó. "A Meta-Omics Analysis Unveils the Shift in Microbial Community Structures and Metabolomics Profiles in Mangrove Sediments Treated with a Selective Actinobacterial Isolation Procedure." Molecules 26, no. 23 (December 2, 2021): 7332. http://dx.doi.org/10.3390/molecules26237332.

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Mangrove sediment ecosystems in the coastal areas of the Yucatan peninsula are unique environments, influenced by their karstic origin and connection with the world’s largest underground river. The microbial communities residing in these sediments are influenced by the presence of mangrove roots and the trading chemistry for communication between sediment bacteria and plant roots can be targeted for secondary metabolite research. To explore the secondary metabolite production potential of microbial community members in mangrove sediments at the “El Palmar” natural reserve in Sisal, Yucatan, a combined meta-omics approach was applied. The effects of a cultivation medium reported to select for actinomycetes within mangrove sediments’ microbial communities was also analyzed. The metabolome of the microbial communities was analyzed by high-resolution liquid chromatography-tandem mass spectrometry, and molecular networking analysis was used to investigate if known natural products and their variants were present. Metagenomic results suggest that the sediments from “El Palmar” harbor a stable bacterial community independently of their distance from mangrove tree roots. An unexpected decrease in the observed abundance of actinomycetes present in the communities occurred when an antibiotic-amended medium considered to be actinomycete-selective was applied for a 30-day period. However, the use of this antibiotic-amended medium also enhanced production of secondary metabolites within the microbial community present relative to the water control, suggesting the treatment selected for antibiotic-resistant bacteria capable of producing a higher number of secondary metabolites. Secondary metabolite mining of “El Palmar” microbial community metagenomes identified polyketide synthase and non-ribosomal peptide synthetases’ biosynthetic genes in all analyzed metagenomes. The presence of these genes correlated with the annotation of several secondary metabolites from the Global Natural Product Social Molecular Networking database. These results highlight the biotechnological potential of the microbial communities from “El Palmar”, and show the impact selective media had on the composition of communities of actinobacteria.
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Tufail, Azra. "Microbial communities colonising nutrient-enriched marine sediment." Hydrobiologia 148, no. 3 (May 1987): 245–55. http://dx.doi.org/10.1007/bf00017527.

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Dissertations / Theses on the topic "Sediment microbial communities"

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Ruuskanen, Matti Olavi. "Lake Sediment Microbial Communities in the Anthropocene." Thesis, Université d'Ottawa / University of Ottawa, 2019. http://hdl.handle.net/10393/39649.

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Since the Industrial Revolution at the end of the 18th century, anthropogenic changes in the environment have shifted from the local to the global scale. Even remote environments such as the high Arctic are vulnerable to the effects of climate change. Similarly, anthropogenic mercury (Hg) has had a global reach because of atmospheric transport and deposition far from emission point sources. Whereas some effects of climate change are visible through melting permafrost, or toxic effects of Hg at higher trophic levels, the often-invisible changes in microbial community structures and functions have received much less attention. With recent and drastic warming-related changes in Arctic watersheds, previously uncharacterized phylogenetic and functional diversity in the sediment communities might be lost forever. The main objectives of my thesis were to uncover how microbial community structure, functional potential and the evolution of mercury specific functions in lake sediments in northern latitudes (>54ºN) are affected by increasing temperatures and Hg deposition. To address these questions, I examined environmental DNA from sediment core samples and high-throughput sequencing to reconstruct the community composition, functional potential, and evolutionary responses to historical Hg loading. In my thesis I show that the microbial community in Lake Hazen (NU, Canada) sediments is structured by redox gradients and pH. Furthermore, the microbes in this phylogenetically diverse community contain genomic features which might represent adaptations to the cold and oligotrophic conditions. Finally, historical Hg pollution from anthropogenic sources has likely affected the evolution of microbial Hg resistance and this deposition can be tracked using sediment DNA on the Northern Hemisphere. My thesis underscores the importance of using culture-independent methods to reconstruct the structure, functional potential and evolution of environmental microbial communities.
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Ogilvie, Lesley Ann. "Quantifying the effects of metals on estuarine sediment microbial communities." Thesis, University of East Anglia, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.410312.

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Sackett, Joshua David. "Comparative microbial ecology of sediment-associated microbial communities from anthropogenically and endogenously metal impacted systems." Thesis, University of Colorado at Denver, 2015. http://pqdtopen.proquest.com/#viewpdf?dispub=1598320.

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Microorganisms, particularly the Bacteria, are differentially impacted by metal toxicities, and will respond very quickly to changes in their environment, making them ideal bioindicators of environmental health. In this study, we evaluated the sediment-associated bacterial diversity of fifty-seven samples collected from twenty-four anthropogenically and endogenously metal impacted, geographically distinct sites in the Colorado Mineral Belt, and elucidated the factors that correlated with observed differences in the bacterial community structure. Overall, the geochemistry of all sites distinguished anthropogenic from endogenous sources of metal impact. Anthropogenic samples, on average, had higher concentrations of total recoverable and dissolved sodium and magnesium, and lower concentrations of aluminum and zinc, compared to the endogenous samples. Bacterial communities from both anthropogenically and endogenously metal impacted sites were characterized using Illumina high-throughput amplicon sequencing of the V4 region of the 16S rRNA gene. Overall, bacterial communities were remarkably diverse, with endogenously metal impacted sediments having higher diversity compared to anthropogenic sediments. The Actinobacteria and Betaproteobacteria dominated anthropogenic samples, and the Acidobacteria and Deltaproteobacteria dominated endogenous samples. Clustering of bacterial communities based on membership and structure (presence/absence and relative abundance of particular taxa, respectively) also distinguished samples based on their source of metal impact. Analysis of similarity (ANOSIM) tests indicated a significant difference between bacterial community structure based on source of metal impact (weighted UniFrac RANOSIM = 0.746, p = 0.001). Mantel tests indicated that total recoverable magnesium concentrations accounted for ∼54% of variance in community structure of all bacterial communities in the study. Dissolved aluminum concentrations accounted for ∼71% of the variation in all communities with an anthropogenic source of metal, and dissolved aluminum concentrations also accounted for ∼41% of the variation in bacterial communities with endogenous sources of metal impact.

This study provides one of the first direct comparisons between microbial community structures of sediments based on source of metal impact. This study is also one of the first comprehensive characterizations of bacterial communities from naturally occurring iron fen systems.

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Hernandez, Sandra Alicia Santillan. "Determination of the Effect of Pesticides on Microbial Communities in Estuarine Sediment using Fingerprinting Techniques." Thesis, University of East Anglia, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.514278.

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Radl, Viviane. "Influence of trenbolone on the structural and functional diversity of microbial communities from a lake sediment." [S.l.] : [s.n.], 2005. http://deposit.ddb.de/cgi-bin/dokserv?idn=978952626.

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Orland, Chloé Shoshana Jessica. "Assembly and functioning of microbial communities along terrestrial resource gradients in boreal lake sediments." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/284909.

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Terrestrial inputs of organic matter contribute greatly to the functioning of aquatic ecosystems, subsidizing between 30-70% of secondary production. This contribution of terrestrial resources is especially important in boreal lakes that are largely nutrient-poor and thus more responsive to these additions. Yet the mechanisms underlying initial processing of terrestrial resources by microbial communities at the base of lake food webs remain poorly understood. With this in mind, this thesis aims to advance our understanding of lake sediment microbial community assembly and functioning along abiotic gradients, primarily reflecting variation in terrestrial organic matter inputs that are predicted to increase with future environmental change. Chapter 1 reviews current knowledge on the terrestrial support of lake food webs and highlights gaps in understanding the factors influencing the microbial processing of terrestrial resources. It also provides an overview of metagenomics methods for microbial community analysis and their development over the course of the thesis. Chapter 2 tests how much of ecosystem functioning is explained by microbial community structure relative to other ecosystem properties such as the present-day and past environment. Theory predicts that ecosystem functioning, here measured as CO2 production, should increase with diversity, but the individual and interactive effects of other ecosystem properties on ecosystem functioning remain unresolved. Chapter 3 further questions the importance of microbial diversity for ecosystem functioning by asking whether more diverse microbial communities stabilize ubiquitous functions like CO2 production and microbial abundances through time. It also aims to identify the biotic and abiotic mechanisms underlying positive diversity-stability relationships. Chapter 4 then explores how microbial communities assemble and colonize sediments with varying types and amounts of terrestrial organic matter in three different lakes over a two-month period. Understanding how microbial communities change in relation to sediment and lake conditions can help predict downstream ecosystem functions. Finally, Chapter 5 discusses the main findings of the thesis and ends with proposed avenues for future research.
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Jeanbille, Mathilde. "Réponse des consortia microbiens benthiques à une contamination chronique aux hydrocarbures." Thesis, Pau, 2015. http://www.theses.fr/2015PAUU3043/document.

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Les communautés microbiennes procèdent au recyclage des nutriments et à la degradation de la matière organique, et sont ainsi essentielles aux cycles biogéochimiques dans le sédiment et plus largement dans les océans. La contamination chronique aux hydrocarbures représente près de 80% des déversements totaux dans les océans. Toutefois, en comparaison des marées noires, son impact sur les communautés microbiennes est encore mal compris. Dans cette étude, nous avons d’abord utilisé une approche de type méta-analyse pour élucider l’effet global de la contamination aux hydrocarbures dans différents habitats. La réponse des communautés bactériennes à la contamination s’est révélée être dépendante du type d’habitat, les sols étant plus impactés que d’autres habitats, comme par exemple les sédiments marins. Nous nous sommes ensuite intéressés aux communautés microbiennes des trois domaines du vivant de sédiments côtiers provenant des côtes méditerranéennes et atlantiques. La contamination chronique n’influençait que marginallement les communautés benthiques, et la diversité alpha n’était pas réduite dans les sédiments contaminés. Cedendant, la comparaison des réseaux de co-occurrence des échantillons contaminés et non-contaminés a montré que le réseau des communautés contaminées présentait une topologie différente, indiquant une vulnérabilité plus importante à d’éventuelles perturbations environnementales. Des indicateurs potentiels de la contamination identifiés avec la méta-analyse ont été ciblés pour étudier l’impact de la contamination chronique aux hydrocarbures sur les services écologiques qu’ils assurent (i.e. la dégradation de la matière organique et des hydrocarbures) en utillisant la technique de Micro-FISH
Within the sediment, microbial communities play a pivotal role by driving essential processes such as nutrient cycling and organic matter degradation. Chronic hydrocarbons contamination represents almost 80% of the total input in the oceans. However, as compared to oil spills, its impact on microbial communities remains poorly understood. In this study, we first used a meta-analysis approach to decipher the global effect of hydrocarbons contamination in different habitats. Bacterial community response to the contamination was found to be dependant of the habitat studied, with soils being more impacted than other habitats, like marine sediments. Because bacteria are in interactions with other important members of microbial communities such as Archaea and Eukaryotes, we focused on microbial communities from the three domains of life in coastal marine sediments from the Mediterrranean and the French Atlantic coasts. Independently of the domains of life, chronic hydrocarbons contamination appeared to be a poor driver of communities structuration, and alpha diversity was not reduced in contaminated sediments. However, the comparison of co-occurences networks of contaminated and non-contaminated samples showed that the network from the contaminated samples exhibited a different topology, which suggests a higher vulnerability to eventual environmental perturbations. Potential indicators species identified using the meta-analysis approach were targeted to study the impact of chronic contamination on the ecological services they provide (i.e. organic matter and hydrocarbons degradation) using the Micro-FISH method
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Louvado, António Miguel de Oliveira. "Oil descontamination by benthic microbial communities." Doctoral thesis, Universidade de Aveiro, 2018. http://hdl.handle.net/10773/23525.

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Doutoramento em Biologia
Os sedimentos marinhos são um reservatório de hidrocarbonetos petrogénicos libertados naturalmente ou acidentalmente para o ambiente marinho. Nos sedimentos marinhos, os hidrocarbonetos são usados como fonte de carbono e energia por comunidades bacterianas complexas. Contudo, a eficiência de biodegradação poderá ser limitada por fatores ambientais. Este trabalho aborda o previsível impacto das condições particulares do mar profundo, da acidificação dos oceanos e da adição de dispersantes químicos nos processos de biodegradação de hidrocarbonetos em ambientes marinhos. Numa primeira fase, a função de destoxificação primária das bactérias degradadoras de hidrocarbonetos aromáticos policíclicos (HAP) nos sedimentos do mar profundo foi avaliado através de uma compilação de informação disponível na literatura científica e também através de uma análise dependente do cultivo envolvendo culturas de enriquecimento de sedimentos de vulcões de lama do mar profundo. Posteriormente, o impacto interativo da acidificação do oceano e da contaminação por hidrocarbonetos petrogénicos em comunidades bacterianas bênticas foi avaliado, em experiências de simulação multifatorial em sistema de microcosmo previamente executadas, com sedimentos subsuperficiais estuarinos. Finalmente, foi executado uma experiência multifatorial em sistema de microcosmos para avaliar o impacto da aplicação de dispersantes químicos em situações simuladas de derrame de hidrocarbonetos em sedimentos estuarinos portuários. Os resultados obtidos, através da análise da fração cultivável, indicam que nos sedimentos do mar profundo a comunidade bacteriana degradadora de HAP é distinta da encontrada noutros sedimentos marinhos devido à predominância de bactérias relacionadas com o género Bacillus. Nos ensaios de microcosmos, apesar das diferenças entre os cenários testados, as comunidades bacterianas revelaram-se em geral, estáveis. Nos sedimentos subsuperficiais estuarinos, as alterações abióticas impostas foram provavelmente atenuadas pela barreira sedimentar sobrejacente e a comunidade bacteriana pareceu ser estável em termos de estrutura e atividade. Do mesmo modo, a dispersão química de hidrocarbonetos petrogénicos, apesar de aumentar a biodisponibilidade de PAH, não alterou significativamente a composição das comunidades bacteriana de sedimentos superficiais estuarinos. Possivelmente, a exposição prévia do sedimento portuário a poluição por hidrocarbonetos poderá ter condicionado a resposta da comunidade bêntica bacteriana à contaminação por petróleo. Em conclusão, a degradação bacteriana de hidrocarbonetos é um processo ubíquo em sedimentos marinhos e as comunidades bacterianas degradadoras revelam elevada estabilidade relativamente à variação de fatores ambientais.
The marine sediment compartment is a key sink for naturally and accidentally released oil hydrocarbons in the marine environment. Here, complex communities of interacting bacterial species will efficiently use oil hydrocarbons as sources of carbon and energy. However, the efficiency of the biodegradation process can be limited by some near-future scenarios. This work addresses different environmental scenarios regarding oil hydrocarbon biodegradation in marine sediments. First, the role of bacteria as primary detoxifiers of polycyclic aromatic hydrocarbons in deep-sea sediments was evaluated through the compilation of available data and through a culture-dependent analysis of enrichment cultures derived mud volcano sediments. Next, the impact of the interactive effects of ocean acidification and oil hydrocarbon contamination was further analyzed in subsurface estuarine sediments. Finally, the impact of chemically dispersed oil in estuarine port sediments is evaluated through a multi-factorial microcosm simulation. Results show that , in deep sea mud volcano sediments, the culturable fraction of the PAH-degrading bacterial community seems distinct from other environments, with a predominance of Bacillus-like bacteria. In the microcosmbased assays, despite the differences between them, the overall bacterial community exhibit a reliable stability. In subsurface sediments, abiotic changes tested were possibly attenuated by the superficial sediment barrier and bacterial seem stable to environmental changes. Also, the chemical dispersion of oil, despite enhancing PAH concentration, did not impose significant alterations to the bacterial community composition at the marine sediment surface. The potential pre-exposure of the port sediment to oil hydrocarbon pollution may have preconditioned the response of the benthic bacterial communities to oil contamination. In conclusion, oil-hydrocarbon biodegradation is ubiquitous and communities exhibit a structural stability to environmental changes.
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Looft, Torey P. "MOLECULAR CHARACTERIZATION OF MICROBIAL COMMUNITIES IN LAKE ERIE SEDIMENTS." Bowling Green State University / OhioLINK, 2005. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1131392301.

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Bessette, Sandrine. "Identification des communautés microbiennes des lobes terminaux du système turbiditique du Congo." Thesis, Brest, 2016. http://www.theses.fr/2016BRES0022/document.

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L'éventail sous-marin profond du Congo, situé sur la marge continentale Congo-Angolaise (côte Ouest Africaine, Océan Atlantique Equatorial Sud) représente un écosystème sédimentaire marin profond unique.Celui-ci est caractérisé par de forts apports en matière organique provenant du fleuve Congo, qui se déversent le long du canyon et au travers de systèmes chenal Jevées actuels jusque dans les zones les plus profondes (5 000 m) où se développe le système des lobes.L'objectif de cette thèse est d'étudier la distribution spatiale et la diversité phylogénétique et fonctionnelle des communautés archéennes et bactériennes en relation avec les caractéristiques et les contraintes de I'environnement.Cette étude a permis de mettre en évidence une distribution géographique régionale et locale des communautés microbiennes contraintes par la distance des différents lobes par rapport à l'embouchure du chenal. La distribution des communautés microbiennes est liée à la disponibilité en accepteurs et donneurs d'électrons issus de la diagénèse précoce de la matière organique. La composition et l'identité taxonomique de ces communautés microbiennes sont comparables aux communautés rencontrées dans des sédiments marins et des zones d'émission de fluides froids riches en méthane.Cette étude révèle également des densités cellulaires relativement élevées de bactéries méthanotrophes aérobies associées à différents habitats sédimentaires particuliers, colonisés par des bivalves Vesicomyidae, des tapis microbiens et des sédiments réduits caractéristiques des environnements d'émissions de fluides froids riches en méthane et hydrogène sulfuré. Ces communautés sont non seulement apparentées à celles rencontrées dans des habitats d'émissions de fluides froids, mais également à celles des habitats terrestres, malgré la distance ~ 1000 km des côtes Africaines.Les travaux menés au cours de cette thèse montrent l'intérêt des études pluridisciplinaires pour comprendre la diversité et le fonctionnement des écosystèmes dans les lobes terminaux du système turbiditique du Congo et apportent de nouvelles informations sur la diversité des microorganismes peu explorée dans les éventails sous-marins profonds
The Congo deep sea fan, located in the Congo-Angola continental margin (West African coast, Equatorial South Atlantic Ocean) represents a unique deep-sea sedimentary ecosystem. It is characterized by high organic matter inputs from the Congo River, that flow along a canyon and through presently active channel system-lifted into the deeper areas (5 000 m) where the lobes system develops.The aim of this thesis is to study the spatial distribution as well as the phylogenetic and functional diversity of archaeal and bacterial communities in relation with environmental characteristics and constraints of the terminal lobes of the Congo deep see fan, one of the largest submarine fan systems in the world.This study highlights geographical distribution of microbial communities constrained by the distal and proximal distance of the different lobes from the Congo river's channel mouth as well as linked to the electron donor and acceptor availability from organic matter diagenesis. This study revealed quite high abundance of aerobic methane oxidizing bacteria cells at peculiar sedimentary habitats dominated by Vesicomyid bivalves, microbial mats and reduced sediments typical of cold-seep environments. These communities are not only related to the ones encountered in cold seeps, but also to the ones in terrestrial habitats despite an approximately distance of 1000 km offshore the African coast.This thesis underlines the interest of pluridisciplinary studies to understand the ecosystem diversity and functioning in the terminal lobes of the Congo turbiditic system and provides further insights into the underexplored microbial diversity from deep-sea fans
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Books on the topic "Sediment microbial communities"

1

Braddock, Joan F. Petroleum hydrocarbon-degrading microbial communities in Beaufort-Chukchi Sea sediments. Fairbanks, AK: Coastal Marine Institute, School of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 2004.

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Braddock, Joan F. Petroleum hydrocarbon-degrading microbial communities in Beaufort-Chukchi Sea sediments. Fairbanks, AK: Coastal Marine Institute, School of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 2004.

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Sheppard, Charles R. C., Simon K. Davy, Graham M. Pilling, and Nicholas A. J. Graham. Microbial, microalgal and planktonic reef life. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198787341.003.0005.

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Microbes, including bacteria, archaea, viruses, fungi, protozoans and microalgae, are the most abundant and arguably the most important members of coral reef communities. They occur in the water column and sediment, and in association with other reef organisms. This chapter describes the abundance, diversity, function and productivity of microbes, with an emphasis on free-living types. They are key to recycling and retention of organic matter via the ‘microbial loop’, and are an important food source for larger reef organisms. The metazoan zooplankton are also described, including larvae of most reef invertebrates and fish. They are described in terms of their duration in the plankton, their settlement behaviour (e.g. that of coral larvae), their daily migration patterns and their role as a food source for larger organisms. Their importance for inter-reef connectivity is discussed.
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Microbial Communities in Coastal Sediments. Elsevier, 2021. http://dx.doi.org/10.1016/c2017-0-02214-0.

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Thanga, Salom. Microbial Communities in Coastal Sediments: Structure and Functions. Elsevier, 2020.

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Thanga, Salom. Microbial Communities in Coastal Sediments: Structure and Functions. Elsevier, 2020.

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Taberlet, Pierre, Aurélie Bonin, Lucie Zinger, and Eric Coissac. Some early landmark studies. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198767220.003.0011.

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Chapter 11 entitled “Some early landmark studies” revisits several seminal articles that paved the way for the field of eDNA research. It first evokes the paper that first coined the expression “environmental DNA” in the late 1980s. Then, it describes how eDNA was first exploited in the early 1990s to reveal an unsuspected microbial diversity that morphology- or cultivation-based methods had failed to reach. In the late 1990s, microbiologists began to explore in several pioneer papers the functional insight provided by “metagenomes” (i.e., the collective genomes found in eDNA samples). In the 2000s, eDNA analysis was finally extended to macroorganisms. Chapter 11 reports such a use in two very different contexts (i.e., the detection of a contemporary invasive species, the bullfrog, and the reconstruction of past plant and animal communities from sediment and permafrost samples).
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Gautam, Susma Bhattarai. Performance Assessment and Enrichment of Anaerobic Methane Oxidizing Microbial Communities from Marine Sediments in Bioreactors. Taylor & Francis Group, 2018.

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Gautam, Susma Bhattarai. Performance Assessment and Enrichment of Anaerobic Methane Oxidizing Microbial Communities from Marine Sediments in Bioreactors. Taylor & Francis Group, 2018.

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Gautam, Susma Bhattarai. Performance Assessment and Enrichment of Anaerobic Methane Oxidizing Microbial Communities from Marine Sediments in Bioreactors. Taylor & Francis Group, 2018.

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Book chapters on the topic "Sediment microbial communities"

1

Teske, Andreas. "Marine Deep Sediment Microbial Communities." In The Prokaryotes, 123–38. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-30123-0_42.

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Sobecky, P. A. "Plasmid ecology of marine sediment microbial communities." In Molecular Ecology of Aquatic Communities, 9–18. Dordrecht: Springer Netherlands, 1999. http://dx.doi.org/10.1007/978-94-011-4201-4_2.

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Montague, Clay L., Mary Paulic, and Trimbak M. Parchure. "The stability of sediments containing microbial communities: Initial experiments with varying light intensity." In Nearshore and Estuarine Cohesive Sediment Transport, 348–59. Washington, D. C.: American Geophysical Union, 1993. http://dx.doi.org/10.1029/ce042p0348.

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EL Bour, Monia, Micha Rijkenberg, Aymen Saadi, Maria Virginia Martins, and Noureddine Zaaboub. "Characterization of Deep-Sea Sediment Microbial Communities from Different Mediterranean Sea Regions." In Recent Advances in Environmental Science from the Euro-Mediterranean and Surrounding Regions (2nd Edition), 2095–101. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-51210-1_328.

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Geliashvili, Natia, Ekaterine Jaiani, Marina Tediashvili, and Nils-Kåre Birkeland. "Taxonomic Characteristics of Dominant Microbial Communities in Hot Spring Sediments in Western Georgia." In Microorganisms for Sustainability, 87–96. Singapore: Springer Singapore, 2021. http://dx.doi.org/10.1007/978-981-16-3731-5_5.

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Malek, Harrabi, Diogo A. M. Alexandrino, Marisa R. Almeida, Ana P. Mucha, Fatma Aloulou, Elluech Boubaker, and Maria F. Carvalho. "Biodegradation of the Antibiotics Oxytetracycline and Enrofloxacin by Microbial Communities from Douro Estuary (Portugal) Sediments." In Recent Advances in Environmental Science from the Euro-Mediterranean and Surrounding Regions, 595–96. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-70548-4_180.

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MacGregor, B. J., K. Ravenschlag, and R. Amann. "Nucleic Acid-Based Techniques for Analyzing the Diversity, Structure, and Function of Microbial Communities in Marine Waters and Sediments." In Ocean Margin Systems, 419–38. Berlin, Heidelberg: Springer Berlin Heidelberg, 2002. http://dx.doi.org/10.1007/978-3-662-05127-6_26.

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Singh, Arvind K., Angela Sherry, Neil D. Gray, Martin D. Jones, Wilfred F. M. Röling, and Ian M. Head. "How Specific Microbial Communities Benefit the Oil Industry: Dynamics of Alcanivorax spp. in Oil-Contaminated Intertidal Beach Sediments Undergoing Bioremediation." In Applied Microbiology and Molecular Biology in Oilfield Systems, 199–209. Dordrecht: Springer Netherlands, 2010. http://dx.doi.org/10.1007/978-90-481-9252-6_24.

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Vincent, Salom Gnana Thanga, Tim Jennerjahn, and Kumarasamy Ramasamy. "Source and composition of organic matter and its role in designing sediment microbial communities." In Microbial Communities in Coastal Sediments, 1–45. Elsevier, 2021. http://dx.doi.org/10.1016/b978-0-12-815165-5.00001-7.

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Bhattarai, S., C. Cassarini, Z. Naangmenyele, E. R. Rene, G. Gonzalez-Gil, and G. Esposito. "Microbial Sulfate Reducing Activities in Anoxic Sediment from Marine Lake Grevelingen." In Performance Assessment and Enrichment of Anaerobic Methane Oxidising Microbial Communities from Marine Sediments in Bioreactors, 83–106. CRC Press, 2018. http://dx.doi.org/10.1201/9780429448027-3.

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Conference papers on the topic "Sediment microbial communities"

1

Kaptein, Victoria R., Michel Pelletier, and Mark R. Noll. "VARIATIONS IN STREAM SEDIMENT MICROBIAL COMMUNITIES ACROSS A NATURAL CLIMATE GRADIENT IN SOUTHEASTERN PUERTO RICO." In GSA Annual Meeting in Indianapolis, Indiana, USA - 2018. Geological Society of America, 2018. http://dx.doi.org/10.1130/abs/2018am-321833.

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WANG, Li, Rulong Liu, and Jiasong Fang. "Transitions in microbial communities along two sediment corescollected from the landward walls of the New Britain trench." In Goldschmidt2021. France: European Association of Geochemistry, 2021. http://dx.doi.org/10.7185/gold2021.3910.

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Kuzikova, Irina, Irina Kuzikova, Vera Safronova, Vera Safronova, Nadezda Medvedeva, and Nadezda Medvedeva. "IMPACT OF NONYLPHENOL ON THE PHYSIOLOGICAL ACTIVITY OF FUNGI FROM THE COASTAL AREA OF THE GULF OF FINLAND." In Managing risks to coastal regions and communities in a changing world. Academus Publishing, 2017. http://dx.doi.org/10.31519/conferencearticle_5b1b93c5890b52.86067390.

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Nonylphenol (NP) is the most abundant environmental estrogen listed as one of the priority hazardous substances in the Water Framework Directive (EC 2000) and the priority pollutant of Baltic Sea (HELCOM 2010). The present study aims to compare the effects of technical nonylphenol (tNP) on the cellulase, amylase and protease activity of the terrestrial fungal strains played a significant role in aquatic ecosystems due to their high adaptive capacity and a large range of functional activity. The study also attempts to understand the mechanisms behind the varying sensitivity of the terrestrial fungi to tNP. The fungal strains were isolated from the bottom sediments of the coastal area of the eastern part of the Gulf of Finland. The terrestrial fungi were identified based on their morphological characteristics and nucleotide sequence analysis of internal transcribed space region. One reason for significant differences in sensitivity to the toxicant studied among the fungi is the change in the fungal cell permeability, in particular in cell membrane permeability, induced by NP. Environmentally relevant concentrations of tNP cause significant changes in activity of hydrolytic enzymes in the terrestrial fungi Aspergillus tubingensis, Penicillium expansum, Penicillium glabrum, and Cadophora fastigiata involved in organic matter degradation in bottom sediments. There can be increasing or decreasing trend, depending on both the type of enzyme and the tNP concentration. The revealed changes may disrupt the destructive processes in bottom sediments, as well as succession and stability of microbial communities functioning in the aquatic environment. It was found that tNP contributes to the activation of proteolytic enzymes, considered as potential fungal virulence factors. This may lead to emergence fungal strains with enhanced virulence in aquatic microbiocenoses. The investigations of the physiological responses of terrestrial fungi under nonylphenol will be important for biochemical processes dynamics and their environmental consequences evaluation.
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Kuzikova, Irina, Irina Kuzikova, Vera Safronova, Vera Safronova, Nadezda Medvedeva, and Nadezda Medvedeva. "IMPACT OF NONYLPHENOL ON THE PHYSIOLOGICAL ACTIVITY OF FUNGI FROM THE COASTAL AREA OF THE GULF OF FINLAND." In Managing risks to coastal regions and communities in a changing world. Academus Publishing, 2017. http://dx.doi.org/10.21610/conferencearticle_58b431765a62a.

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Nonylphenol (NP) is the most abundant environmental estrogen listed as one of the priority hazardous substances in the Water Framework Directive (EC 2000) and the priority pollutant of Baltic Sea (HELCOM 2010). The present study aims to compare the effects of technical nonylphenol (tNP) on the cellulase, amylase and protease activity of the terrestrial fungal strains played a significant role in aquatic ecosystems due to their high adaptive capacity and a large range of functional activity. The study also attempts to understand the mechanisms behind the varying sensitivity of the terrestrial fungi to tNP. The fungal strains were isolated from the bottom sediments of the coastal area of the eastern part of the Gulf of Finland. The terrestrial fungi were identified based on their morphological characteristics and nucleotide sequence analysis of internal transcribed space region. One reason for significant differences in sensitivity to the toxicant studied among the fungi is the change in the fungal cell permeability, in particular in cell membrane permeability, induced by NP. Environmentally relevant concentrations of tNP cause significant changes in activity of hydrolytic enzymes in the terrestrial fungi Aspergillus tubingensis, Penicillium expansum, Penicillium glabrum, and Cadophora fastigiata involved in organic matter degradation in bottom sediments. There can be increasing or decreasing trend, depending on both the type of enzyme and the tNP concentration. The revealed changes may disrupt the destructive processes in bottom sediments, as well as succession and stability of microbial communities functioning in the aquatic environment. It was found that tNP contributes to the activation of proteolytic enzymes, considered as potential fungal virulence factors. This may lead to emergence fungal strains with enhanced virulence in aquatic microbiocenoses. The investigations of the physiological responses of terrestrial fungi under nonylphenol will be important for biochemical processes dynamics and their environmental consequences evaluation.
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5

Otte, Julia, Frank Wenzhöfer, and Jessica Volz. "Spatial distribution of metal-cycling microbial communities along geochemical gradients in sediments of polymetallic nodule fields, Eastern Pacific Ocean." In Goldschmidt2021. France: European Association of Geochemistry, 2021. http://dx.doi.org/10.7185/gold2021.6967.

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Arias-Thode, Y. Meriah, Ken Richter, Adriane Wotawa-Bergen, D. Bart Chadwick, Jinjun Kan, and Kenneth Nealson. "Development of microbial fuel cell prototypes for examination of the temporal and spatial response of anodic bacterial communities in marine sediments." In OCEANS 2011 - SPAIN. IEEE, 2011. http://dx.doi.org/10.1109/oceans-spain.2011.6003535.

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Reports on the topic "Sediment microbial communities"

1

Sobecky, Patricia A. Plasmid Diversity and Horizontal Transfer in Marine Sediment Microbial Communities. Fort Belvoir, VA: Defense Technical Information Center, February 2002. http://dx.doi.org/10.21236/ada399348.

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Marsh, Terence L. Phylogenetic & Physiological Profiling of Microbial Communities of Contaminated Soils/Sediments: Identifying Microbial consortia... Office of Scientific and Technical Information (OSTI), May 2004. http://dx.doi.org/10.2172/824396.

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Arias-Thode, Y. M., Ken Richter, Adriane Wotawa-Bergen, D. B. Chadwick, Jinjun Kan, and Kenneth Nealson. Development of Microbial Fuel Cell Prototypes for Examination of the Temporal and Spatial Response of Anodic Bacterial Communities in Marine Sediments. Fort Belvoir, VA: Defense Technical Information Center, January 2014. http://dx.doi.org/10.21236/ada610308.

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