scholarly journals Microarray-Based Characterization of Microbial Community Functional Structure and Heterogeneity in Marine Sediments from the Gulf of Mexico

2008 ◽  
Vol 74 (14) ◽  
pp. 4516-4529 ◽  
Author(s):  
Liyou Wu ◽  
Laurie Kellogg ◽  
Allan H. Devol ◽  
James M. Tiedje ◽  
Jizhong Zhou
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Gulf Of Mexico ◽  
Marine Sediments ◽  
Microbial Community Structure ◽  
Metal Resistance ◽  
Functional Gene ◽  
Functional Genes ◽  
Contaminant Degradation ◽  
Carbon Degradation

ABSTRACT Marine sediments of coastal margins are important sites of carbon sequestration and nitrogen cycling. To determine the metabolic potential and structure of marine sediment microbial communities, two cores were collected each from the two stations (GMT at a depth of 200 m and GMS at 800 m) in the Gulf of Mexico, and six subsamples representing different depths were analyzed from each of these two cores using functional gene arrays containing ∼2,000 probes targeting genes involved in carbon fixation; organic carbon degradation; contaminant degradation; metal resistance; and nitrogen, sulfur, and phosphorous cycling. The geochemistry was highly variable for the sediments based on both site and depth. A total of 930 (47.1%) probes belonging to various functional gene categories showed significant hybridization with at least 1 of the 12 samples. The overall functional gene diversity of the samples from shallow depths was in general lower than those from deep depths at both stations. Also high microbial heterogeneity existed in these marine sediments. In general, the microbial community structure was more similar when the samples were spatially closer. The number of unique genes at GMT increased with depth, from 1.7% at 0.75 cm to 18.9% at 25 cm. The same trend occurred at GMS, from 1.2% at 0.25 cm to 15.2% at 16 cm. In addition, a broad diversity of geochemically important metabolic functional genes related to carbon degradation, nitrification, denitrification, nitrogen fixation, sulfur reduction, phosphorus utilization, contaminant degradation, and metal resistance were observed, implying that marine sediments could play important roles in biogeochemical cycling of carbon, nitrogen, phosphorus, sulfate, and various metals. Finally, the Mantel test revealed significant positive correlations between various specific functional genes and functional processes, and canonical correspondence analysis suggested that sediment depth, PO4 3−, NH4 +, Mn(II), porosity, and Si(OH)4 might play major roles in shaping the microbial community structure in the marine sediments.

Nutrients, microbial community structure and functional gene abundance of rhizosphere and bulk soils of halophytes

2015 ◽  
Vol 91 ◽  
pp. 16-26 ◽  
Author(s):  
Doongar R. Chaudhary ◽  
Ritesh K. Gautam ◽  
Basit Yousuf ◽  
Avinash Mishra ◽  
Bhavanath Jha
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Functional Gene ◽  
Gene Abundance ◽  
Functional Gene Abundance

scholarly journals Changes in Soil Microbial Community Structure and Functional Genes Following with Different Functional Traits Species Afforestation

2021 ◽  
Author(s):  
Yang Gao ◽  
Xiuwei Wang ◽  
Zijun Mao ◽  
Liu Yang ◽  
Zhiyan Jiang ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Soil Nitrogen ◽  
Microbial Community Structure ◽  
Soil Microbial Community ◽  
Functional Genes ◽  
Soil Microbial Community Structure ◽  
Soil Microbial ◽  
Evergreen Conifer ◽  
Mixed Plantation

Abstract Aim Soil microbial community structure and functional genes are critical to the cycling of carbon and nutrients in forest soils. As afforestation practices increasingly promote different functional traits tree species, it becomes critical to understand how they influences soil microbial community structures and functional genes, which directly influence soil biogeochemical processes. Methods We used fungi ITS and bacteria 16S rDNA to investigate soil microbial communities and functional genes 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) to compare with two 1:1 mixed-species plantations (P. sibirica and L. gmelinii, P. sibirica and B. platyphylla).Results 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 bacteria communities were strongly related to soil nitrogen. Microbial co-occurrence patterns varied according to plantation types and altered soil nutrient cycling. Microbial communities in forest plantations of conifer-angiosperm mixed plantation contribute to soil nitrogen fixation and coniferous mixed plantation contribute to soil carbon fixation. Conclusions Our results provide a comparative study of the soil microbial ecology in afforestation of different functional trains species. This knowledge enhances the understanding of the relative control of soil microbial community structure.

scholarly journals COMPARISON OF MICROBIAL COMMUNITY STRUCTURE IN COASTAL MARINE SEDIMENTS OF THREE AUSTRAL SUMMERS IN ADMIRALTY BAY, KING GEORGE ISLAND

2016 ◽  
pp. 74-77
Author(s):  
Diego Castillo Franco ◽  
Rubens Tadeu Delgado Duarte ◽  
Amanda Gonçalves Bendia ◽  
Cristina Rossi Nakayama ◽  
Vivian Helena Pellizari
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Marine Sediments ◽  
Microbial Community Structure ◽  
King George Island ◽  
Coastal Marine Sediments ◽  
Admiralty Bay ◽  
Coastal Marine

scholarly journals Extent of the annual Gulf of Mexico hypoxic zone influences microbial community structure

2018 ◽  
Author(s):  
Lauren Gillies Campbell ◽  
J. Cameron Thrash ◽  
Nancy N. Rabalais ◽  
Olivia U. Mason
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gulf Of Mexico ◽  
Dissolved Oxygen ◽  
Microbial Community Structure ◽  
Rrna Gene ◽  
Hypoxic Zone ◽  
Low Do

AbstractRich geochemical datasets generated over the past 30 years have provided fine-scale resolution on the northern Gulf of Mexico (nGOM) coastal hypoxic (≤ 2 mg of O2 L-1) zone. In contrast, little is known about microbial community structure and activity in the hypoxic zone despite the implication that microbial respiration is responsible for forming low dissolved oxygen (DO) conditioXSns. Here, we hypothesized that the extent of the hypoxic zone is a driver in determining microbial community structure, and in particular, the abundance of ammonia-oxidizing archaea (AOA). Samples collected across the shelf for two consecutive hypoxic seasons in July 2013 and 2014 were analyzed using 16S rRNA gene sequencing, oligotyping, microbial co-occurrence analysis and quantification of thaumarchaeal 16S rRNA and archaeal ammonia-monooxygenase (amoA) genes. In 2014 Thaumarchaeota were enriched and inversely correlated with DO while Cyanobacteria, Acidimicrobiia and Proteobacteria where more abundant in oxic samples compared to hypoxic. Oligotyping analysis of Nitrosopumilus 16S rRNA gene sequences revealed that one oligotype was significantly inversely correlated with dissolved oxygen (DO) in both years and that low DO concentrations, and the high Thaumarchaeota abundances, influenced microbial co-occurrence patterns. Taken together, the data demonstrated that the extent of hypoxic conditions could potentially influence patterns in microbial community structure, with two years of data revealing that the annual nGOM hypoxic zone is emerging as a low DO adapted AOA hotspot.

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