Environmental factors shaping microbial community structure in salt marsh sediments

ABSTRACT Denitrifying microbial communities and denitrification in salt marsh sediments may be affected by many factors, including environmental conditions, nutrient availability, and levels of pollutants. The objective of this study was to examine how microbial community composition and denitrification enzyme activities (DEA) at a California salt marsh with high nutrient loading vary with such factors. Sediments were sampled from three elevations, each with different inundation and vegetation patterns, across 12 stations representing various salinity and nutrient conditions. Analyses included determination of cell abundance, total and denitrifier community compositions (by terminal restriction fragment length polymorphism), DEA, nutrients, and eluted metals. Total bacterial (16S rRNA) and denitrifier (nirS) community compositions and DEA were analyzed for their relationships to environmental variables and metal concentrations via multivariate direct gradient and regression analyses, respectively. Community composition and DEA were highly variable within the dynamic salt marsh system, but each was strongly affected by elevation (i.e., degree of inundation) and carbon content as well as by selected metals. Carbon content was highly related to elevation, and the relationships between DEA and carbon content were found to be elevation specific when evaluated across the entire marsh. There were also lateral gradients in the marsh, as evidenced by an even stronger association between community composition and elevation for a marsh subsystem. Lastly, though correlated with similar environmental factors and selected metals, denitrifier community composition and function appeared uncoupled in the marsh.

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Using Bioinformatics to Quantify the Variability and Diversity of the Microbial Community Structure in Pond Ecosystems of a Subtropical Catchment

Current Bioinformatics ◽

10.2174/1574893615999200422120819 ◽

2020 ◽

Vol 15 ◽

Author(s):

Jiaogen Zhou ◽

Yang Wang ◽

Qiuliang Lei

Keyword(s):

Community Structure ◽

Microbial Community ◽

Environmental Factors ◽

Microbial Communities ◽

Microbial Community Structure ◽

Fish Farming ◽

Water Bodies ◽

Fish Pond ◽

P Fractions ◽

Pond Ecosystems

Background: In rural China, many natural water bodies and farmlands have been converted to fish farming ponds as an economic development strategy. There is still a limited understanding of how the diversity and structure of microbial communities change in natural and managed fish pond ecosystems. Objective: We aimed to identify the changes of the diversity and structure of microbial community and driving mechanism in pond ecosystems. Methods: The datasets of 16S rRNA amplicon sequencing and the concentrations of N and P fractions were achieved in water samplers of pond ecosystems. Bioinformatics analysis was used to analyze the diversity and structure of the microbial communities. Results: Our results indicated that the diversity and structure of the microbial communities in the natural ponds were significantly different from ones in managed fish ponds. The nutrients of N and P and water environmental factors were responsible for 46.3% and 19.5% of the changes in the structure and diversity of the microbial community, respectively. Conclusion: The N and P fractions and water environmental factors influenced the microbial community structure and diversity in pond ecosystems. Fish farming indirectly affected the microbial community by altering the contents of N and P fractions in water bodies of ponds when a natural pond was converted to a managed fish pond. Conclusion: The N and P fractions and water environmental factors influenced the microbial community structure and diversity in pond ecosystems. Fish farming indirectly affected the microbial community by altering the contents of N and P fractions in water bodies of ponds when a natural pond was converted to a managed fish pond.

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Environmental Factors Shape Water Microbial Community Structure and Function in Shrimp Cultural Enclosure Ecosystems

Frontiers in Microbiology ◽

10.3389/fmicb.2017.02359 ◽

2017 ◽

Vol 8 ◽

Cited By ~ 48

Author(s):

Dongwei Hou ◽

Zhijian Huang ◽

Shenzheng Zeng ◽

Jian Liu ◽

Dongdong Wei ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Environmental Factors ◽

Microbial Community Structure ◽

Structure And Function ◽

And Function

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Salt marsh pore water geochemistry does not correlate with microbial community structure

Estuarine Coastal and Shelf Science ◽

10.1016/j.ecss.2004.09.001 ◽

2005 ◽

Vol 62 (1-2) ◽

pp. 233-251 ◽

Cited By ~ 71

Author(s):

Carla M. Koretsky ◽

Philippe Van Cappellen ◽

Thomas J. DiChristina ◽

Joel E. Kostka ◽

Kristi L. Lowe ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Salt Marsh ◽

Pore Water ◽

Microbial Community Structure ◽

Water Geochemistry ◽

Pore Water Geochemistry

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Ecological Effects of Heavy Metal Pollution on Soil Microbial Community Structure and Diversity on Both Sides of a River around a Mining Area

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph17165680 ◽

2020 ◽

Vol 17 (16) ◽

pp. 5680

Author(s):

Xingqing Zhao ◽

Jian Huang ◽

Xuyan Zhu ◽

Jinchun Chai ◽

Xiaoli Ji

Keyword(s):

Heavy Metal ◽

Community Structure ◽

Microbial Community ◽

Environmental Factors ◽

Microbial Communities ◽

Microbial Community Structure ◽

Metal Pollution ◽

Heavy Metal Pollution ◽

Mining Area ◽

Soil Microbial

The objectives of this study were to understand the characteristics of heavy metal pollution caused by mining activities on the two sides of the Shun’an river and the response of soil microorganisms to the habitats by different contamination levels and vegetation. This paper selected soil samples from the banks of the Shun’an River near the Shizishan mining area, which is at the left of the river, in Tongling, Anhui Province, China. Using Illumina MiSeq 2500 technology, we analyzed the relationship between environmental factors and microbial communities. As the distance from the mining area increased, the heavy metal comprehensive pollution and potential risk value decreased. Additionally, the pollution severity and risk value of the left bank, where the mining area lies, were generally higher than those of the right bank. Because the symmetric sampling points on both banks of the river had similar planting types, their environmental factors and microbial community structure were similar and clustered. However, under different vegetation, the paddy soils tended to have a higher nutrient content and community richness and diversity than the vegetable fields or the abandoned land. It was found that soil microbial communities in this area were mostly affected by pH and Nemerow pollution index (PN). The pH significantly affected the abundance and structure of most microorganisms. In addition, Proteobacteria, Acidobacteria, and Bacteroidetes had significant tolerance to Zn, Pb, and Cd. By exploring the potential use of these tolerant microorganisms, we seek to provide strains and the theoretical basis for the bioremediation of areas contaminated by heavy metal.

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Changes in the Microbial Community Diversity of Oil Exploitation

Genes ◽

10.3390/genes10080556 ◽

2019 ◽

Vol 10 (8) ◽

pp. 556 ◽

Cited By ~ 4

Author(s):

Jingjing Liu ◽

Jing Wu ◽

Jiawei Lin ◽

Jian Zhao ◽

Tianyi Xu ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Environmental Factors ◽

Oil Recovery ◽

Microbial Community Structure ◽

Storage Tank ◽

Oil Production ◽

Operational Taxonomic Unit ◽

Community Diversity ◽

Microbial Resources

To systematically evaluate the ecological changes of an active offshore petroleum production system, the variation of microbial communities at several sites (virgin field, wellhead, storage tank) of an oil production facility in east China was investigated by sequencing the V3 to V4 regions of 16S ribosomal ribonucleic acid (rRNA) of microorganisms. In general, a decrease of microbial community richness and diversity in petroleum mining was observed, as measured by operational taxonomic unit (OTU) numbers, α (Chao1 and Shannon indices), and β (principal coordinate analysis) diversity. Microbial community structure was strongly affected by environmental factors at the phylum and genus levels. At the phylum level, virgin field and wellhead were dominated by Proteobacteria, while the storage tank had higher presence of Firmicutes (29.3–66.9%). Specifically, the wellhead displayed a lower presentence of Proteobacteria (48.6–53.4.0%) and a higher presence of Firmicutes (24.4–29.6%) than the virgin field. At the genus level, the predominant genera were Ochrobactrum and Acinetobacter in the virgin field, Lactococcus and Pseudomonas in the wellhead, and Prauseria and Bacillus in the storage tank. Our study revealed that the microbial community structure was strongly affected by the surrounding environmental factors, such as temperature, oxygen content, salinity, and pH, which could be altered because of the oil production. It was observed that the various microbiomes produced surfactants, transforming the biohazard and degrading hydro-carbon. Altering the microbiome growth condition by appropriate human intervention and taking advantage of natural microbial resources can further enhance oil recovery technology.

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