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Journal articles on the topic 'Microbial community structure'

Author: Grafiati

Published: 4 June 2021

Last updated: 2 February 2022

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1

Peralta, Ariane L., Jeffrey W. Matthews, and Angela D. Kent. "Microbial Community Structure and Denitrification in a Wetland Mitigation Bank." Applied and Environmental Microbiology 76, no. 13 (May 7, 2010): 4207–15. http://dx.doi.org/10.1128/aem.02977-09.

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ABSTRACT Wetland mitigation is implemented to replace ecosystem functions provided by wetlands; however, restoration efforts frequently fail to establish equivalent levels of ecosystem services. Delivery of microbially mediated ecosystem functions, such as denitrification, is influenced by both the structure and activity of the microbial community. The objective of this study was to compare the relationship between soil and vegetation factors and microbial community structure and function in restored and reference wetlands within a mitigation bank. Microbial community composition was assessed using terminal restriction fragment length polymorphism targeting the 16S rRNA gene (total bacteria) and the nosZ gene (denitrifiers). Comparisons of microbial function were based on potential denitrification rates. Bacterial community structures differed significantly between restored and reference wetlands; denitrifier community assemblages were similar among reference sites but highly variable among restored sites throughout the mitigation bank. Potential denitrification was highest in the reference wetland sites. These data demonstrate that wetland restoration efforts in this mitigation bank have not successfully restored denitrification and that differences in potential denitrification rates may be due to distinct microbial assemblages observed in restored and reference (natural) wetlands. Further, we have identified gradients in soil moisture and soil fertility that were associated with differences in microbial community structure. Microbial function was influenced by bacterial community composition and soil fertility. Identifying soil factors that are primary ecological drivers of soil bacterial communities, especially denitrifying populations, can potentially aid the development of predictive models for restoration of biogeochemical transformations and enhance the success of wetland restoration efforts.

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Okita, Noriko, Toshihiro Hoaki, Sinya Suzuki, and Masashi Hatamoto. "Characteristics of Microbial Community Structure at the Seafloor Surface of the Nankai Trough." Journal of Pure and Applied Microbiology 13, no. 4 (December 30, 2019): 1917–28. http://dx.doi.org/10.22207/jpam.13.4.04.

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3

Cheng, C., D. Zhao, D. Lv, S. Li, and G. Du. "Comparative study on microbial community structure across orchard soil, cropland soil, and unused soil." Soil and Water Research 12, No. 4 (October 9, 2017): 237–45. http://dx.doi.org/10.17221/177/2016-swr.

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We examined the effects of three different soil conditions (orchard soil, cropland soil, unused soil) on the functional diversity of soil microbial communities. The results first showed that orchard and cropland land use significantly changed the distribution and diversity of soil microbes, particularly at surface soil layers. The richness index (S) and Shannon diversity index (H) of orchard soil microbes were significantly higher than the indices of the cropland and unused soil treatments in the 0–10 cm soil layer, while the S and H indices of cropland soil microbes were the highest in 10–20 cm soil layers. Additionally, the Simpson dominance index of cropland soil microbial communities was the highest across all soil layers. Next, we found that carbon source differences in soil layers under the three land use conditions can mainly be attributed to their carbohydrate and polymer composition, indicating that they are the primary cause of the functional differences in microbial communities under different land uses. In conclusion, orchard and cropland soil probably affected microbial distribution and functional diversity due to differences in vegetation cover, cultivation, and management measures.

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4

Pérez-Brandán, C., J. Huidobro, M. Galván, S. Vargas-Gil, and Meriles JM. "Relationship between microbial functions and community structure following agricultural intensification in South American Chaco." Plant, Soil and Environment 62, No. 7 (July 24, 2016): 321–28. http://dx.doi.org/10.17221/19/2016-pse.

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5

Findlay, Robert H., Christine Yeates, Meredith A. J. Hullar, David A. Stahl, and Louis A. Kaplan. "Biome-Level Biogeography of Streambed Microbiota." Applied and Environmental Microbiology 74, no. 10 (March 31, 2008): 3014–21. http://dx.doi.org/10.1128/aem.01809-07.

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ABSTRACT A field study was conducted to determine the microbial community structures of streambed sediments across diverse geographic and climatic areas. Sediment samples were collected from three adjacent headwater forest streams within three biomes, eastern deciduous (Pennsylvania), southeastern coniferous (New Jersey), and tropical evergreen (Guanacaste, Costa Rica), to assess whether there is biome control of stream microbial community structure. Bacterial abundance, microbial biomass, and bacterial and microbial community structures were determined using classical, biochemical, and molecular methods. Microbial biomass, determined using phospholipid phosphate, was significantly greater in the southeastern coniferous biome, likely due to the smaller grain size, higher organic content, and lower levels of physical disturbance of these sediments. Microbial community structure was determined using phospholipid fatty acid (PLFA) profiles and bacterial community structure from terminal restriction fragment length polymorphism and edited (microeukaryotic PLFAs removed) PLFA profiles. Principal component analysis (PCA) was used to investigate patterns in total microbial community structure. The first principal component separated streams based on the importance of phototrophic microeukaryotes within the community, while the second separated southeastern coniferous streams from all others based on increased abundance of fungal PLFAs. PCA also indicated that within- and among-stream variations were small for tropical evergreen streams and large for southeastern coniferous streams. A similar analysis of bacterial community structure indicated that streams within biomes had similar community structures, while each biome possessed a unique streambed community, indicating strong within-biome control of stream bacterial community structure.

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6

Tankere, S. P. C., D. G. Bourne, F. L. L. Muller, and V. Torsvik. "Microenvironments and microbial community structure in sediments." Environmental Microbiology 4, no. 2 (February 2002): 97–105. http://dx.doi.org/10.1046/j.1462-2920.2002.00274.x.

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7

Bach, Lisbet Holm, John-Arvid Grytnes, Rune Halvorsen, and Mikael Ohlson. "Tree influence on soil microbial community structure." Soil Biology and Biochemistry 42, no. 11 (November 2010): 1934–43. http://dx.doi.org/10.1016/j.soilbio.2010.07.002.

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8

SCHIMEL, JOSHUA P., and JAY GULLEDGE. "Microbial community structure and global trace gases." Global Change Biology 4, no. 7 (October 1998): 745–58. http://dx.doi.org/10.1046/j.1365-2486.1998.00195.x.

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9

Fuhrman, Jed A. "Microbial community structure and its functional implications." Nature 459, no. 7244 (May 2009): 193–99. http://dx.doi.org/10.1038/nature08058.

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10

Gao, Yang, Xiuwei Wang, Zijun Mao, Liu Yang, Zhiyan Jiang, Xiangwei Chen, and Doug P. Aubrey. "Changes in Soil Microbial Community Structure Following Different Tree Species Functional Traits Afforestation." Forests 12, no. 8 (July 30, 2021): 1018. http://dx.doi.org/10.3390/f12081018.

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The soil microbial community structure is critical to the cycling of carbon and nitrogen in forest soils. As afforestation practices increasingly promote different functional traits of tree species, it has become critical to understand how they influence soil microbial community structures, which directly influence soil biogeochemical processes. We used fungi ITS and bacteria 16S rDNA to investigate soil microbial community structures in three monoculture plantations consisting of a non-native evergreen conifer (Pinus sibirica), a native deciduous conifer (Larix gmelinii), and a native deciduous angiosperm (Betula platyphylla) and compared them with two 1:1 mixed-species plantations (P. sibirica and L. gmelinii, P. sibirica and B. platyphylla). The fungal community structure of the conifer–angiosperm mixed plantation was similar to that of the non-native evergreen conifer, and the bacterial community structure was similar to that of the angiosperm monoculture plantation. Fungal communities were strongly related to tree species, but bacterial communities were strongly related to soil nitrogen. The co-occurrence networks were more robust in the mixed plantations, and the microbial structures associated with soil carbon and nitrogen were significantly increased. Our results provide a comparative study of the soil microbial ecology in response to afforestation of species with different functional traits and enhance the understanding of factors controlling the soil microbial community structure.

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11

Lourdes, Vital, Narvaez Jose A, Cruz Maria Antonia, Ortiz Eyra L, Sanchez Eric, and Mendoza Alberto. "Unravelling the composition of soil belowground microbial community before sowing transgenic cotton." Plant, Soil and Environment 63, No. 11 (November 20, 2017): 512–18. http://dx.doi.org/10.17221/523/2017-pse.

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Soils harbour enormously diverse bacterial communities that interact specifically with plants generating beneficial interactions between them. This study was the first approach to assess bacterial communities before sowing with three cotton genotypes, including both transgenic and conventional ones. The structure of bacterial communities was identified using the next generation sequencing analysis, ion torrent PGM (Personal Genome Machine™) sequencer technology, based on the V2–V3 16S rRNA gene region. Quantitative insights into microbial ecology pipeline were used to identify the structure and diversity of bacterial communities in bulk soil samples collected in the northeast of Mexico. Bulk soil textures and chemical properties, including most nutrients, were homogeneous in these bulk soil samples. Relative abundance analysis showed similar bacterial community structures. Dominant taxonomic phyla were Proteobacteria, Firmicutes, Acidobacteria, Actinobacteria, Gemmatimonadetes and Bacteroidetes, whereas the main families were Bacillaceae, Chitinophagaceae and Rhodospirillaceae with an abundance average of BS1 (bulk soil sample), BS2 and BS3 (24.85, 19.74 and 19.71%, respectively). Alpha diversity analysis showed a high diversity (Shannon and Simpson index) and a large value of the observed species found in bulk soils samples. These results allowed establishing the previous bacterial structural community in an unused soil before sowing it with a transgenic crop for the first time.

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12

Guo, Xuechao, Yu Miao, Bing Wu, Lin Ye, Haiyan Yu, Su Liu, and Xu-xiang Zhang. "Correlation between microbial community structure and biofouling as determined by analysis of microbial community dynamics." Bioresource Technology 197 (December 2015): 99–105. http://dx.doi.org/10.1016/j.biortech.2015.08.049.

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13

Buyer, Jeffrey S., Daniel P. Roberts, and Estelle Russek-Cohen. "Soil and plant effects on microbial community structure." Canadian Journal of Microbiology 48, no. 11 (November 1, 2002): 955–64. http://dx.doi.org/10.1139/w02-095.

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We investigated the effects of two different plant species (corn and soybean) and three different soil types on microbial community structure in the rhizosphere. Our working hypothesis was that the rhizosphere effect would be strongest on fast-growing aerobic heterotrophs, while there would be little or no rhizosphere effect on oligotrophic and other slow-growing microorganisms. Culturable bacteria and fungi had larger population densities in the rhizosphere than in bulk soil. Communities were characterized by soil fatty acid analysis and by substrate utilization assays for bacteria and fungi. Fatty acid analysis revealed a very strong soil effect but little plant effect on the microbial community, indicating that the overall microbial community structure was not affected by the rhizosphere. There was a strong rhizosphere effect detected by the substrate utilization assay for fast-growing aerobic heterotrophic bacterial community structure, with soil controls and rhizosphere samples clearly distinguished from each other. There was a much weaker rhizosphere effect on fungal communities than on bacterial communities as measured by the substrate utilization assays. At this coarse level of community analysis, the rhizosphere microbial community was impacted most by soil effects, and the rhizosphere only affected a small portion of the total bacteria.Key words: rhizosphere, microbial community, fatty acid, substrate utilization.

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14

Almatouq, Abdullah, Akintunde O. Babatunde, Mishari Khajah, Gordon Webster, and Mohammad Alfodari. "Microbial community structure of anode electrodes in microbial fuel cells and microbial electrolysis cells." Journal of Water Process Engineering 34 (April 2020): 101140. http://dx.doi.org/10.1016/j.jwpe.2020.101140.

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15

Humphries, J. A., A. M. H. Ashe, J. A. Smiley, and C. G. Johnston. "Microbial community structure and trichloroethylene degradation in groundwater." Canadian Journal of Microbiology 51, no. 6 (June 1, 2005): 433–39. http://dx.doi.org/10.1139/w05-025.

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Trichloroethylene (TCE) is a prevalent contaminant of groundwater that can be cometabolically degraded by indigenous microbes. Groundwater contaminated with TCE from a US Department of Energy site in Ohio was used to characterize the site-specific impact of phenol on the indigenous bacterial community for use as a possible remedial strategy. Incubations of14C-TCE-spiked groundwater amended with phenol showed increased TCE mineralization compared with unamended groundwater. Community structure was determined using DNA directly extracted from groundwater samples. This DNA was then analyzed by amplified ribosomal DNA restriction analysis. Unique restriction fragment length polymorphisms defined operational taxonomic units that were sequenced to determine phylogeny. DNA sequence data indicated that known TCE-degrading bacteria including relatives of Variovorax and Burkholderia were present in site water. Diversity of the amplified microbial rDNA clone library was lower in phenol-amended communities than in unamended groundwater (i.e., having Shannon–Weaver diversity indices of 2.0 and 2.2, respectively). Microbial activity was higher in phenol-amended ground water as determined by measuring the reduction of 2-(p-iodophenyl)-3(p-nitrophenyl)-5-phenyl tetrazolium chloride. Thus phenol amendments to groundwater correlated with increased TCE mineralization, a decrease in diversity of the amplified microbial rDNA clone library, and increased microbial activity.Key words: community structure, trichloroethylene, degradation, groundwater.

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16

Palaniveloo, Kishneth, Muhammad Azri Amran, Nur Azeyanti Norhashim, Nuradilla Mohamad-Fauzi, Fang Peng-Hui, Low Hui-Wen, Yap Kai-Lin, et al. "Food Waste Composting and Microbial Community Structure Profiling." Processes 8, no. 6 (June 22, 2020): 723. http://dx.doi.org/10.3390/pr8060723.

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Over the last decade, food waste has been one of the major issues globally as it brings a negative impact on the environment and health. Rotting discharges methane, causing greenhouse effect and adverse health effects due to pathogenic microorganisms or toxic leachates that reach agricultural land and water system. As a solution, composting is implemented to manage and reduce food waste in line with global sustainable development goals (SDGs). This review compiles input on the types of organic composting, its characteristics, physico-chemical properties involved, role of microbes and tools available in determining the microbial community structure. Composting types: vermi-composting, windrow composting, aerated static pile composting and in-vessel composting are discussed. The diversity of microorganisms in each of the three stages in composting is highlighted and the techniques used to determine the microbial community structure during composting such as biochemical identification, polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE), terminal restriction fragment length polymorphism (T-RFLP) and single strand-conformation polymorphism (SSCP), microarray analysis and next-generation sequencing (NGS) are discussed. Overall, a good compost, not only reduces waste issues, but also contributes substantially to the economic and social sectors of a nation.

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17

Koh, Hyeon Woo, Sundas Rani, Han-Bit Hwang, and Soo-Je Park. "Microbial community structure analysis from Jeju marine sediment." Korean Journal of Microbiology 52, no. 3 (September 30, 2016): 375–79. http://dx.doi.org/10.7845/kjm.2016.6040.

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18

Li, Hui, Dianfeng Liu, Bin Lian, Yuan Sheng, and Hailiang Dong. "Microbial Diversity and Community Structure on Corroding Concretes." Geomicrobiology Journal 29, no. 5 (June 2012): 450–58. http://dx.doi.org/10.1080/01490451.2011.581328.

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19

Chen, Jianwei, Anna Hanke, Halina E. Tegetmeyer, Ines Kattelmann, Ritin Sharma, Emmo Hamann, Theresa Hargesheimer, et al. "Impacts of chemical gradients on microbial community structure." ISME Journal 11, no. 4 (January 17, 2017): 920–31. http://dx.doi.org/10.1038/ismej.2016.175.

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20

Hodge, Angela, and Alastair H. Fitter. "Microbial mediation of plant competition and community structure." Functional Ecology 27, no. 4 (October 15, 2012): 865–75. http://dx.doi.org/10.1111/1365-2435.12002.

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21

SLABBERT, ETIENNE, RAPHAEL Y. KONGOR, KAREN J. ESLER, and KARIN JACOBS. "Microbial diversity and community structure in Fynbos soil." Molecular Ecology 19, no. 5 (March 2010): 1031–41. http://dx.doi.org/10.1111/j.1365-294x.2009.04517.x.

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22

Edlund, Anna, Terence Soule, Sara Sjöling, and Janet K. Jansson. "Microbial community structure in polluted Baltic Sea sediments." Environmental Microbiology 8, no. 2 (February 2006): 223–32. http://dx.doi.org/10.1111/j.1462-2920.2005.00887.x.

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23

Brown, Mark V., Gayle K. Philip, John A. Bunge, Matthew C. Smith, Andrew Bissett, Federico M. Lauro, Jed A. Fuhrman, and Stuart P. Donachie. "Microbial community structure in the North Pacific ocean." ISME Journal 3, no. 12 (July 23, 2009): 1374–86. http://dx.doi.org/10.1038/ismej.2009.86.

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24

Huang, Jie. "Gallstone composition and microbial community structure in gallstones." World Chinese Journal of Digestology 22, no. 17 (2014): 2467. http://dx.doi.org/10.11569/wcjd.v22.i17.2467.

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25

Lladó, Salvador, Rubén López-Mondéjar, and Petr Baldrian. "Drivers of microbial community structure in forest soils." Applied Microbiology and Biotechnology 102, no. 10 (March 30, 2018): 4331–38. http://dx.doi.org/10.1007/s00253-018-8950-4.

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26

Kim, Min-Jung, Chang-Wook Jeon, Gyongjun Cho, Da-Ran Kim, Yong-Bum Kwack, and Youn-Sig Kwak. "Comparison of Microbial Community Structure in Kiwifruit Pollens." Plant Pathology Journal 34, no. 2 (April 1, 2018): 143–49. http://dx.doi.org/10.5423/ppj.nt.12.2017.0281.

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27

Ma, Qiao, Yuanyuan Qu, Wenli Shen, Jingwei Wang, Zhaojing Zhang, Xuwang Zhang, Hao Zhou, and Jiti Zhou. "Activated sludge microbial community responses to single-walled carbon nanotubes: community structure does matter." Water Science and Technology 71, no. 8 (March 3, 2015): 1235–40. http://dx.doi.org/10.2166/wst.2015.095.

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The ecological effects of carbon nanotubes (CNTs) have been a worldwide research focus due to their extensive release and accumulation in environment. Activated sludge acting as an important gathering place will inevitably encounter and interact with CNTs, while the microbial responses have been rarely investigated. Herein, the activated sludges from six wastewater treatment plants were acclimated and treated with single-walled carbon nanotubes (SWCNTs) under identical conditions. Illumina high-throughput sequencing was applied to in-depth analyze microbial changes and results showed SWCNTs differently perturbed the alpha diversity of the six groups (one increase, two decrease, three no change). Furthermore, the microbial community structures were shifted, and specific bacterial performance in each group was different. Since the environmental and operational factors were identical in each group, it could be concluded that microbial responses to SWCNTs were highly depended on the original community structures.

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28

Keinänen, Minna M., Pertti J. Martikainen, and Merja H. Kontro (Suutari). "Microbial community structure and biomass in developing drinking water biofilms." Canadian Journal of Microbiology 50, no. 3 (March 1, 2004): 183–91. http://dx.doi.org/10.1139/w04-005.

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Traditional techniques to study microbes, such as culturable counts, microbial biomass, or microbial activity, do not give information on the microbial ecology of drinking water systems. The aim of this study was to analyze whether the microbial community structure and biomass differed in biofilms collected from two Finnish drinking water distribution systems (A and B) receiving conventionally treated (coagulation, filtration, disinfection) surface water. Phospholipid fatty acid methyl esters (PLFAs) and lipopolysaccharide 3-hydroxy fatty acid methyl esters (LPS 3-OH-FAs) were analyzed from biofilms as a function of water residence time and development time. The microbial communities were rather stabile through the distribution systems, as water residence time had minor effects on PLFA profiles. In distribution system A, the microbial community structure in biofilms, which had developed in 6 weeks, was more complex than those grown for 23 or 40 weeks. The microbial communities between the studied distribution systems differed, possibly reflecting the differences in raw water, water purification processes, and distribution systems. The viable microbial biomass, estimated on the basis of PLFAs, increased with increasing water residence time in both distribution systems. The quantitative amount of LPS 3-OH-FAs increased with increasing development time of biofilms of distribution system B. In distribution system A, LPS 3-OH-FAs were below the detection limit.Key words: biofilm, distribution system, 3-hydroxy fatty acid, microbial community, PLFA.

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29

Bier, Raven L., Emily S. Bernhardt, Claudia M. Boot, Emily B. Graham, Edward K. Hall, Jay T. Lennon, Diana R. Nemergut, et al. "Linking microbial community structure and microbial processes: an empirical and conceptual overview." FEMS Microbiology Ecology 91, no. 10 (September 13, 2015): fiv113. http://dx.doi.org/10.1093/femsec/fiv113.

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30

Timmers, Ruud A., Michael Rothballer, David P. B. T. B. Strik, Marion Engel, Stephan Schulz, Michael Schloter, Anton Hartmann, Bert Hamelers, and Cees Buisman. "Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell." Applied Microbiology and Biotechnology 94, no. 2 (February 25, 2012): 537–48. http://dx.doi.org/10.1007/s00253-012-3894-6.

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31

Xiao, Xi-yuan, Ming-wei Wang, Hui-wen Zhu, Zhao-hui Guo, Xiao-qing Han, and Peng Zeng. "Response of soil microbial activities and microbial community structure to vanadium stress." Ecotoxicology and Environmental Safety 142 (August 2017): 200–206. http://dx.doi.org/10.1016/j.ecoenv.2017.03.047.

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32

Sohn, Soo-In, Young-Ju Oh, Jae-Hyung Ahn, Hyeon-jung Kang, Woo-Suk Cho, Yoonsung Cho, and Bum Kyu Lee. "Effects of Disease Resistant Genetically Modified Rice on Soil Microbial Community Structure According to Growth Stage." Korean Journal of Environmental Agriculture 38, no. 3 (September 30, 2019): 185–96. http://dx.doi.org/10.5338/kjea.2019.38.3.18.

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33

Bock, Nicholas, France Van Wambeke, Moïra Dion, and Solange Duhamel. "Microbial community structure in the western tropical South Pacific." Biogeosciences 15, no. 12 (June 29, 2018): 3909–25. http://dx.doi.org/10.5194/bg-15-3909-2018.

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Abstract. Oligotrophic regions play a central role in global biogeochemical cycles, with microbial communities in these areas representing an important term in global carbon budgets. While the general structure of microbial communities has been well documented in the global ocean, some remote regions such as the western tropical South Pacific (WTSP) remain fundamentally unexplored. Moreover, the biotic and abiotic factors constraining microbial abundances and distribution remain not well resolved. In this study, we quantified the spatial (vertical and horizontal) distribution of major microbial plankton groups along a transect through the WTSP during the austral summer of 2015, capturing important autotrophic and heterotrophic assemblages including cytometrically determined abundances of non-pigmented protists (also called flagellates). Using environmental parameters (e.g., nutrients and light availability) as well as statistical analyses, we estimated the role of bottom–up and top–down controls in constraining the structure of the WTSP microbial communities in biogeochemically distinct regions. At the most general level, we found a “typical tropical structure”, characterized by a shallow mixed layer, a clear deep chlorophyll maximum at all sampling sites, and a deep nitracline. Prochlorococcus was especially abundant along the transect, accounting for 68 ± 10.6 % of depth-integrated phytoplankton biomass. Despite their relatively low abundances, picophytoeukaryotes (PPE) accounted for up to 26 ± 11.6 % of depth-integrated phytoplankton biomass, while Synechococcus accounted for only 6 ± 6.9 %. Our results show that the microbial community structure of the WTSP is typical of highly stratified regions, and underline the significant contribution to total biomass by PPE populations. Strong relationships between N2 fixation rates and plankton abundances demonstrate the central role of N2 fixation in regulating ecosystem processes in the WTSP, while comparative analyses of abundance data suggest microbial community structure to be increasingly regulated by bottom–up processes under nutrient limitation, possibly in response to shifts in abundances of high nucleic acid bacteria (HNA).

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Wang, Ji Hua, Jian Fei Guan, Xue Chen Yang, Miao Wang, Shan Shan Zhang, and Wan Tong Gu. "The Influence of Ecological Remediation Process on Bacterial Community Composition in Beishi River Sediment Determined by PCR-DGGE Analysis." Applied Mechanics and Materials 675-677 (October 2014): 102–5. http://dx.doi.org/10.4028/www.scientific.net/amm.675-677.102.

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Pollution of urban river is a major risk to human health and water quality throughout the world. The purpose of this study was to determine the influence of ecological remediation process on sediment bacterial community structure. Three sediment samples in urban river located in Changzhou city, the bacterial community structure was studied in the process of ecological remediation period using denaturing gradient gel electrophoresis (DGGE). The results of the microbial community analysis were related to water environmental parameters through the analysis to investigate the relationship between potential impact of water quality and microbial community structure. As the ecological remediated river, T, DO and COD were the important environmental variables influencing the sediment microbial community composition. Microbial community changes determined by DGGE patterns showed that microbial community structures in the same period did not change further, while those in different period changed continuously. In July 2010, Pseudomonas sp, Escherichia sp, Exiguobacterium sp and Bacillus sp as each point jointly owned. In October 2010, Acinetobacter sp, Clostridiales, Dechloromonas sp and uncultured bacterium were belonged to these three sample sites.

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35

Banning, Natasha C., Deirdre B. Gleeson, Andrew H. Grigg, Carl D. Grant, Gary L. Andersen, Eoin L. Brodie, and D. V. Murphy. "Soil Microbial Community Successional Patterns during Forest Ecosystem Restoration." Applied and Environmental Microbiology 77, no. 17 (July 1, 2011): 6158–64. http://dx.doi.org/10.1128/aem.00764-11.

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ABSTRACTSoil microbial community characterization is increasingly being used to determine the responses of soils to stress and disturbances and to assess ecosystem sustainability. However, there is little experimental evidence to indicate that predictable patterns in microbial community structure or composition occur during secondary succession or ecosystem restoration. This study utilized a chronosequence of developing jarrah (Eucalyptus marginata) forest ecosystems, rehabilitated after bauxite mining (up to 18 years old), to examine changes in soil bacterial and fungal community structures (by automated ribosomal intergenic spacer analysis [ARISA]) and changes in specific soil bacterial phyla by 16S rRNA gene microarray analysis. This study demonstrated that mining in these ecosystems significantly altered soil bacterial and fungal community structures. The hypothesis that the soil microbial community structures would become more similar to those of the surrounding nonmined forest with rehabilitation age was broadly supported by shifts in the bacterial but not the fungal community. Microarray analysis enabled the identification of clear successional trends in the bacterial community at the phylum level and supported the finding of an increase in similarity to nonmined forest soil with rehabilitation age. Changes in soil microbial community structure were significantly related to the size of the microbial biomass as well as numerous edaphic variables (including pH and C, N, and P nutrient concentrations). These findings suggest that soil bacterial community dynamics follow a pattern in developing ecosystems that may be predictable and can be conceptualized as providing an integrated assessment of numerous edaphic variables.

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36

Wu, Ran, Xiaoqin Cheng, and Hairong Han. "The Effect of Forest Thinning on Soil Microbial Community Structure and Function." Forests 10, no. 4 (April 23, 2019): 352. http://dx.doi.org/10.3390/f10040352.

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Microbial communities and their associated enzyme activities play key roles in carbon cycling in ecosystems. Forest thinning is likely to change the soil properties and feedbacks on the structure and function of microbial communities, consequently affecting microbial regulation on the soil carbon process. However, few studies have focused on the mechanism of how thinning affects the quantity and stability of soil carbon. To reveal the influence of thinning on soil carbon and to explore the regulated key factors, this study was conducted in a pure Larix principis-rupprechtii Mayr plantation with different thinning intensity (light, medium, and high) in Shanxi province, China. Soil properties (soil pH, soil water content, soil organic carbon, and soil microbial biomass carbon) were measured. Meanwhile, soil microbial communities were examined with the method of phospholipid fatty acid (PLFA), and soil enzyme activities were measured as indicators of soil microbial functions. The results showed that medium and high thinning has positive effects on soil organic carbon, microbial biomass carbon, soil microbial abundance, and soil enzyme activities. Actinomycetes and gram-negative bacteria were the major factors to affect soil microbial community function relating to carbon decomposition. Soil pH contributed to actinomycetes and gram-negative bacteria through direct influences on arbuscular mycorrhizal fungi. Moreover, there were strong correlations between soil pH and microbial community to control soil carbon turnover. The increasing of soil microbial abundance and the microbial regulation on soil carbon in forest thinning need to be considered for sustainable forest management practices in northern China.

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Chung, Ren-Shih, and Ed-Haun Chang. "Soil microbial community structure and microbial activities in the root zone ofNothapodytes nimmoniana." Soil Science and Plant Nutrition 58, no. 4 (August 2012): 479–91. http://dx.doi.org/10.1080/00380768.2012.702282.

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Jia, Jianna, Yu Tang, Bingfeng Liu, Di Wu, Nanqi Ren, and Defeng Xing. "Electricity generation from food wastes and microbial community structure in microbial fuel cells." Bioresource Technology 144 (September 2013): 94–99. http://dx.doi.org/10.1016/j.biortech.2013.06.072.

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Ahmed, Bulbul, Jean-Baptiste Floc’h, Zakaria Lahrach, and Mohamed Hijri. "Phytate and Microbial Suspension Amendments Increased Soybean Growth and Shifted Microbial Community Structure." Microorganisms 9, no. 9 (August 25, 2021): 1803. http://dx.doi.org/10.3390/microorganisms9091803.

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Phytate represents an organic pool of phosphorus in soil that requires hydrolysis by phytase enzymes produced by microorganisms prior to its bioavailability by plants. We tested the ability of a microbial suspension made from an old growth maple forest’s undisturbed soil to mineralize phytate in a greenhouse trial on soybean plants inoculated or non-inoculated with the suspension. MiSeq Amplicon sequencing targeting bacterial 16S rRNA gene and fungal ITS was performed to assess microbial community changes following treatments. Our results showed that soybean nodulation and shoot dry weight biomass increased when phytate was applied to the nutrient-poor substrate mixture. Bacterial and fungal diversities of the root and rhizosphere biotopes were relatively resilient following inoculation by microbial suspension; however, bacterial community structure was significantly influenced. Interestingly, four arbuscular mycorrhizal fungi (AMF) were identified as indicator species, including Glomus sp., Claroideoglomus etunicatum, Funneliformis mosseae and an unidentified AMF taxon. We also observed that an ericoid mycorrhizal taxon Sebacina sp. and three Trichoderma spp. were among indicator species. Non-pathogenic Planctobacteria members highly dominated the bacterial community as core and hub taxa for over 80% of all bacterial datasets in root and rhizosphere biotopes. Overall, our study documented that inoculation with a microbial suspension and phytate amendment improved soybean plant growth.

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Hussain, Q., G. X. Pan, Y. Z. Liu, A. Zhang, L. Q. Li, X. H. Zhang, and Z. J. Jin. " Microbial community dynamics and function associated with rhizosphere over periods of rice growth." Plant, Soil and Environment 58, No. 2 (March 5, 2012): 55–61. http://dx.doi.org/10.17221/390/2010-pse.

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A field experiment was conducted to illustrate the different degree and dynamics of microbial community structure and function in the rhizosphere across four growing stages (before plantation and three growth stages) using a combination of biochemical (enzyme assay and microbial biomass carbon) and molecular approaches of qPCR and PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis). Rice plant cultivation promoted higher enzyme activities (invertase and urease), microbial biomass carbon (C<sub>mic</sub>), bacterial (16S rRNA) and fungal (ITS rRNA) genes abundances in the rhizosphere compared to unplanted soil. Principal component analyses of PCR-DGGE profile also revealed that structures of bacterial and fungal communities of rice planted soil were well distinct from unplanted soil. Moreover, enzyme activities showed a significant positive correlation with the total microbial biomass in the rhizosphere throughout growth stages of rice plant. Relative fungal: bacterial ratios were significantly higher in rice planted soil compared to unplanted soil, suggesting rice plantation enhanced the fungal community in the rice rhizosphere environment. These results further suggest a significant linkage between the microbial community dynamics and function in the rhizosphere associated with rice plant over time.    

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Tung, Hsin-Hsin, John M. Regan, Richard F. Unz, and Yuefeng F. Xie. "Microbial community structure in a drinking water GAC filter." Water Supply 6, no. 2 (March 1, 2006): 267–71. http://dx.doi.org/10.2166/ws.2006.081.

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The biofilm community structure in a granular activated carbon (GAC) filter was investigated by ribosomal intergenic spacer region analysis (RISA). The results showed that microbial diversity diminished and stabilized with time of filter operation. One bacterium (Hydrogenophaga palleronii) was identified according to its 16S-rRNA sequence. However, this bacterium did not degrade any of the HAAs tested. Another bacterium was isolated from biofilm enrichment cultures and was capable of degrading ClAA and Cl2AA.

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Kim, Jong-Shik, and David E. Crowley. "Size fractionation and microbial community structure of soil aggregates." Journal of Agricultural Chemistry and Environment 02, no. 04 (2013): 75–80. http://dx.doi.org/10.4236/jacen.2013.24011.

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CAI, Wei-Ming, Huai-Ying YAO, Wei-Lin FENG, Qun-Li JIN, Yue-Yan LIU, Nan-Yi LI, and Zhong ZHENG. "Microbial Community Structure of Casing Soil During Mushroom Growth." Pedosphere 19, no. 4 (August 2009): 446–52. http://dx.doi.org/10.1016/s1002-0160(09)60137-5.

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Chen, W., W. Liu, N. Pan, W. Jiao, and M. Wang. "Oxytetracycline on functions and structure of soil microbial community." Journal of soil science and plant nutrition, ahead (2013): 0. http://dx.doi.org/10.4067/s0718-95162013005000076.

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Arsène-Ploetze, Florence, Philippe N. Bertin, and Christine Carapito. "Proteomic tools to decipher microbial community structure and functioning." Environmental Science and Pollution Research 22, no. 18 (December 5, 2014): 13599–612. http://dx.doi.org/10.1007/s11356-014-3898-0.

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Benizri, E., O. Dedourge, C. Dibattista-Leboeuf, S. Piutti, C. Nguyen, and A. Guckert. "Effect of maize rhizodeposits on soil microbial community structure." Applied Soil Ecology 21, no. 3 (October 2002): 261–65. http://dx.doi.org/10.1016/s0929-1393(02)00094-x.

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Landry, Michael R., and David L. Kirchman. "Microbial community structure and variability in the tropical Pacific." Deep Sea Research Part II: Topical Studies in Oceanography 49, no. 13-14 (January 2002): 2669–93. http://dx.doi.org/10.1016/s0967-0645(02)00053-x.

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Griffiths, B. S., K. Ritz, N. Ebblewhite, and G. Dobson. "Soil microbial community structure: Effects of substrate loading rates." Soil Biology and Biochemistry 31, no. 1 (January 1998): 145–53. http://dx.doi.org/10.1016/s0038-0717(98)00117-5.

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Haldeman, Dana L., Penny S. Amy, David Ringelberg, David C. White, Rhea E. Garen, and William C. Ghiorse. "Microbial growth and resuscitation alter community structure after perturbation." FEMS Microbiology Ecology 17, no. 1 (May 1995): 27–38. http://dx.doi.org/10.1111/j.1574-6941.1995.tb00124.x.

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Nunan, Naoise, Brajesh Singh, Eileen Reid, Brian Ord, Artemis Papert, Julie Squires, Jim I. Prosser, Ron E. Wheatley, Jim McNicol, and Peter Millard. "Sheep-urine-induced changes in soil microbial community structure." FEMS Microbiology Ecology 56, no. 2 (May 2006): 310–20. http://dx.doi.org/10.1111/j.1574-6941.2006.00072.x.

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