scholarly journals Microbiome succession during ammonification in eelgrass bed sediments

2017 ◽  
Author(s):  
Cassandra L Ettinger ◽  
Susan L Williams ◽  
Jessica M Abbott ◽  
John J Stachowicz ◽  
Jonathan A Eisen
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Sulfur Metabolism ◽  
Microbial Community Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Ecosystem Functions ◽  
Sediment Samples ◽  
Functional Studies ◽  
Elemental Cycling

Background. Eelgrass (Zostera marina) is a marine angiosperm and foundation species that plays an important ecological role in primary production, food web support, and elemental cycling in coastal ecosystems. As with other plants, the microbial communities living in, on, and near eelgrass are thought to be intimately connected to the ecology and biology of eelgrass. Here we characterized the microbial communities in eelgrass sediments throughout an experiment to quantify the rate of ammonification, the first step in early remineralization of organic matter, or diagenesis, from plots at a field site in Bodega Bay, CA. Methods. Sediment was collected from 72 plots from a 15 month long field experiment in which eelgrass genotypic richness and relatedness were manipulated. In the laboratory, we placed sediment samples (n= 4 per plot) under a N2 atmosphere, incubated them at in situ temperatures (15 oC) and sampled them initially and after 4, 7, 13, and 19 days to determine the ammonification rate. Comparative microbiome analysis using high throughput sequencing of 16S rRNA genes was performed on sediment samples taken initially and at 7, 13 and 19 days to characterize the relative abundances of microbial taxa and how they changed throughout early diagenesis. Results. Within-sample diversity of the sediment microbial communities across all plots decreased after the initial timepoint using both richness based (observed number of OTUs, Chao1) and richness and evenness based diversity metrics (Shannon, Inverse Simpson). Additionally, microbial community composition changed across the different timepoints. Many of the observed changes in relative abundance of taxonomic groups between timepoints appeared driven by sulfur cycling with observed decreases in sulfur reducers (Desulfobacterales) and corresponding increases in sulfide oxidizers (Alteromonadales and Thiotrichales). None of these changes in composition or richness were associated with ammonification rates. Discussion. Overall, our results showed that the microbiome of sediment from different plots followed similar successional patterns, which we surmise to be due to changes related to sulfur metabolism. These large changes likely overwhelmed any potential changes in sediment microbiome related to ammonification rate. We found no relationship between eelgrass presence or genetic composition and the microbiome. This was likely due to our sampling of bulk sediments to measure ammonification rates rather than sampling microbes in sediment directly in contact with the plants and suggests that eelgrass influence on the sediment microbiome may be limited in spatial extent. More in-depth functional studies associated with eelgrass microbiome will be required in order to fully understand the implications of these microbial communities in broader host-plant and ecosystem functions (e.g. elemental cycling and eelgrass-microbe interactions).

scholarly journals Microbiome succession during ammonification in eelgrass bed sediments

2017 ◽  
Author(s):  
Cassandra L Ettinger ◽  
Susan L Williams ◽  
Jessica M Abbott ◽  
John J Stachowicz ◽  
Jonathan A Eisen
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Sulfur Metabolism ◽  
Microbial Community Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Ecosystem Functions ◽  
Sediment Samples ◽  
Functional Studies ◽  
Elemental Cycling

Background. Eelgrass (Zostera marina) is a marine angiosperm and foundation species that plays an important ecological role in primary production, food web support, and elemental cycling in coastal ecosystems. As with other plants, the microbial communities living in, on, and near eelgrass are thought to be intimately connected to the ecology and biology of eelgrass. Here we characterized the microbial communities in eelgrass sediments throughout an experiment to quantify the rate of ammonification, the first step in early remineralization of organic matter, or diagenesis, from plots at a field site in Bodega Bay, CA. Methods. Sediment was collected from 72 plots from a 15 month long field experiment in which eelgrass genotypic richness and relatedness were manipulated. In the laboratory, we placed sediment samples (n= 4 per plot) under a N2 atmosphere, incubated them at in situ temperatures (15 oC) and sampled them initially and after 4, 7, 13, and 19 days to determine the ammonification rate. Comparative microbiome analysis using high throughput sequencing of 16S rRNA genes was performed on sediment samples taken initially and at 7, 13 and 19 days to characterize the relative abundances of microbial taxa and how they changed throughout early diagenesis. Results. Within-sample diversity of the sediment microbial communities across all plots decreased after the initial timepoint using both richness based (observed number of OTUs, Chao1) and richness and evenness based diversity metrics (Shannon, Inverse Simpson). Additionally, microbial community composition changed across the different timepoints. Many of the observed changes in relative abundance of taxonomic groups between timepoints appeared driven by sulfur cycling with observed decreases in sulfur reducers (Desulfobacterales) and corresponding increases in sulfide oxidizers (Alteromonadales and Thiotrichales). None of these changes in composition or richness were associated with ammonification rates. Discussion. Overall, our results showed that the microbiome of sediment from different plots followed similar successional patterns, which we surmise to be due to changes related to sulfur metabolism. These large changes likely overwhelmed any potential changes in sediment microbiome related to ammonification rate. We found no relationship between eelgrass presence or genetic composition and the microbiome. This was likely due to our sampling of bulk sediments to measure ammonification rates rather than sampling microbes in sediment directly in contact with the plants and suggests that eelgrass influence on the sediment microbiome may be limited in spatial extent. More in-depth functional studies associated with eelgrass microbiome will be required in order to fully understand the implications of these microbial communities in broader host-plant and ecosystem functions (e.g. elemental cycling and eelgrass-microbe interactions).

scholarly journals Microbiome succession during ammonification in eelgrass bed sediments

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3674 ◽  
Author(s):  
Cassandra L. Ettinger ◽  
Susan L. Williams ◽  
Jessica M. Abbott ◽  
John J. Stachowicz ◽  
Jonathan A. Eisen
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Sulfur Metabolism ◽  
Microbial Community Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Ecosystem Functions ◽  
Sediment Samples ◽  
Functional Studies ◽  
Elemental Cycling

BackgroundEelgrass (Zostera marina) is a marine angiosperm and foundation species that plays an important ecological role in primary production, food web support, and elemental cycling in coastal ecosystems. As with other plants, the microbial communities living in, on, and near eelgrass are thought to be intimately connected to the ecology and biology of eelgrass. Here we characterized the microbial communities in eelgrass sediments throughout an experiment to quantify the rate of ammonification, the first step in early remineralization of organic matter, also known as diagenesis, from plots at a field site in Bodega Bay, CA.MethodsSediment was collected from 72 plots from a 15 month long field experiment in which eelgrass genotypic richness and relatedness were manipulated. In the laboratory, we placed sediment samples (n = 4 per plot) under a N2atmosphere, incubated them atin situtemperatures (15 °C) and sampled them initially and after 4, 7, 13, and 19 days to determine the ammonification rate. Comparative microbiome analysis using high throughput sequencing of 16S rRNA genes was performed on sediment samples taken initially and at seven, 13 and 19 days to characterize changes in the relative abundances of microbial taxa throughout ammonification.ResultsWithin-sample diversity of the sediment microbial communities across all plots decreased after the initial timepoint using both richness based (observed number of OTUs, Chao1) and richness and evenness based diversity metrics (Shannon, Inverse Simpson). Additionally, microbial community composition changed across the different timepoints. Many of the observed changes in relative abundance of taxonomic groups between timepoints appeared driven by sulfur cycling with observed decreases in predicted sulfur reducers (Desulfobacterales) and corresponding increases in predicted sulfide oxidizers (Thiotrichales). None of these changes in composition or richness were associated with variation in ammonification rates.DiscussionOur results showed that the microbiome of sediment from different plots followed similar successional patterns, which we infer to be due to changes related to sulfur metabolism. These large changes likely overwhelmed any potential changes in sediment microbiome related to ammonification rate. We found no relationship between eelgrass presence or genetic composition and the microbiome. This was likely due to our sampling of bulk sediments to measure ammonification rates rather than sampling microbes in sediment directly in contact with the plants and suggests that eelgrass influence on the sediment microbiome may be limited in spatial extent. More in-depth functional studies associated with eelgrass microbiome will be required in order to fully understand the implications of these microbial communities in broader host-plant and ecosystem functions (e.g., elemental cycling and eelgrass-microbe interactions).

scholarly journals Microbiota variations in Culex nigripalpus disease vector mosquito of West Nile virus and Saint Louis Encephalitis from different geographic origins

PeerJ ◽  
2019 ◽  
Vol 6 ◽  
pp. e6168 ◽  
Author(s):  
Dagne Duguma ◽  
Michael W. Hall ◽  
Chelsea T. Smartt ◽  
Mustapha Debboun ◽  
Josh D. Neufeld
Keyword(s):  
Microbial Communities ◽  
Disease Transmission ◽  
High Throughput Sequencing ◽  
Microbial Community Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
West Nile ◽  
Saint Louis ◽  
Culex Nigripalpus ◽  
Saint Louis Encephalitis

Although mosquito microbiota are known to influence reproduction, nutrition, disease transmission, and pesticide resistance, the relationship between host-associated microbial community composition and geographical location is poorly understood. To begin addressing this knowledge gap, we characterized microbiota associated with adult females of Culex nigripalpus mosquito vectors of Saint Louis Encephalitis and West Nile viruses sampled from three locations in Florida (Vero Beach, Palmetto Inland, and Palmetto Coast). High-throughput sequencing of PCR-amplified 16S rRNA genes demonstrated significant differences among microbial communities of mosquitoes sampled from the three locations. Mosquitoes from Vero Beach (east coast Florida) were dominated by uncultivated Asaia sp. (Alphaproteobacteria), whereas microbiota associated with mosquitoes collected from two mosquito populations at Palmetto (west coast Florida) sites were dominated by uncultured Spironema culicis (Spirochaetes), Salinisphaera hydrothermalis (Gammaproteobacteria), Spiroplasma (Mollicutes), uncultured Enterobacteriaceae, Candidatus Megaira (Alphaproteobacteria; Rickettsiae), and Zymobacter (Gammaproteobacteria). The variation in taxonomic profiles of Cx. nigripalpus gut microbial communities, especially with respect to dominating taxa, is a potentially critical factor in understanding disease transmission and mosquito susceptibility to insecticides among different mosquito populations.

scholarly journals Comprehensive skin microbiome analysis reveals the uniqueness of human skin and evidence for phylosymbiosis within the class Mammalia

2018 ◽  
Vol 115 (25) ◽  
pp. E5786-E5795 ◽  
Author(s):  
Ashley A. Ross ◽  
Kirsten M. Müller ◽  
J. Scott Weese ◽  
Josh D. Neufeld
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Human Skin ◽  
Microbial Community Composition ◽  
Geographic Location ◽  
The Body ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Skin Microbiome ◽  
Skin Microbiota

Skin is the largest organ of the body and represents the primary physical barrier between mammals and their external environment, yet the factors that govern skin microbial community composition among mammals are poorly understood. The objective of this research was to generate a skin microbiota baseline for members of the class Mammalia, testing the effects of host species, geographic location, body region, and biological sex. Skin from the back, torso, and inner thighs of 177 nonhuman mammals was sampled, representing individuals from 38 species and 10 mammalian orders. Animals were sampled from farms, zoos, households, and the wild. The DNA extracts from all skin swabs were amplified by PCR and sequenced, targeting the V3-V4 regions of bacterial and archaeal 16S rRNA genes. Previously published skin microbiome data from 20 human participants, sampled and sequenced using an identical protocol to the nonhuman mammals, were included to make this a comprehensive analysis. Human skin microbial communities were distinct and significantly less diverse than all other sampled mammalian orders. The factor most strongly associated with microbial community data for all samples was whether the host was a human. Within nonhuman samples, host taxonomic order was the most significant factor influencing skin microbiota, followed by the geographic location of the habitat. By comparing the congruence between host phylogeny and microbial community dendrograms, we observed that Artiodactyla (even-toed ungulates) and Perissodactyla (odd-toed ungulates) had significant congruence, providing evidence of phylosymbiosis between skin microbial communities and their hosts.

scholarly journals Reduction of Perchlorate and Nitrate by Microbial Communities in Vadose Soil

2005 ◽  
Vol 71 (7) ◽  
pp. 3928-3934 ◽  
Author(s):  
Mamie Nozawa-Inoue ◽  
Kate M. Scow ◽  
Dennis E. Rolston
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Human Thyroid ◽  
Perchlorate Reduction

ABSTRACT Perchlorate contamination is a concern because of the increasing frequency of its detection in soils and groundwater and its presumed inhibitory effect on human thyroid hormone production. Although significant perchlorate contamination occurs in the vadose (unsaturated) zone, little is known about perchlorate biodegradation potential by indigenous microorganisms in these soils. We measured the effects of electron donor (acetate and hydrogen) and nitrate addition on perchlorate reduction rates and microbial community composition in microcosm incubations of vadose soil. Acetate and hydrogen addition enhanced perchlorate reduction, and a longer lag period was observed for hydrogen (41 days) than for acetate (14 days). Initially, nitrate suppressed perchlorate reduction, but once perchlorate started to be degraded, the process was stimulated by nitrate. Changes in the bacterial community composition were observed in microcosms enriched with perchlorate and either acetate or hydrogen. Denaturing gradient gel electrophoresis analysis and partial sequencing of 16S rRNA genes recovered from these microcosms indicated that formerly reported perchlorate-reducing bacteria were present in the soil and that microbial community compositions were different between acetate- and hydrogen-amended microcosms. These results indicate that there is potential for perchlorate bioremediation by native microbial communities in vadose soil.

scholarly journals The Composition and Primary Metabolic Potential of Microbial Communities Inhabiting the Surface Water in the Equatorial Eastern Indian Ocean

Biology ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 248
Author(s):  
Changling Ding ◽  
Chao Wu ◽  
Congcong Guo ◽  
Jiang Gui ◽  
Yuqiu Wei ◽  
...  
Keyword(s):  
Indian Ocean ◽  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Carbon Fixation ◽  
Calvin Cycle ◽  
Nitrite Reduction ◽  
16S Rrna Genes ◽  
Eastern Indian Ocean ◽  
Rrna Genes ◽  
Metabolic Potential

Currently, there is scant information about the biodiversity and functional diversity of microbes in the eastern Indian Ocean (EIO). Here, we used a combination of high-throughput sequencing of 16S rRNA genes and a metagenomic approach to investigate the microbial population structure and its metabolic function in the equatorial EIO. Our results show that Cyanobacterial Prochlorococcus made up the majority of the population. Interestingly, there were fewer contributions from clades SAR11 (Alphaproteobacteria) and SAR86 (Gammaproteobacteria) to microbial communities than contributions from Prochlorococcus. Based on functional gene analysis, functional genes rbcL, narB, and nasA were relatively abundant among the relevant genes. The abundance of Prochlorococcus implies its typically ecological adaptation in the local ecosystem. The microbial metabolic potential shows that in addition to the main carbon fixation pathway Calvin cycle, the rTCA cycle and the 3-HP/4-HB cycle have potential alternative carbon fixation contributions to local ecosystems. For the nitrogen cycle, the assimilatory nitrate and nitrite reduction pathway is potentially the crucial form of nitrogen utilization; unexpectedly, nitrogen fixation activity was relatively weak. This study extends our knowledge of the roles of microbes in energy and resource cycling in the EIO and provides a foundation for revealing profound biogeochemical processes driven by the microbial community in the ocean.

Seasonal variation of epiphytic bacteria in the phyllosphere of Gingko biloba, Pinus bungeana and Sabina chinensis

2020 ◽  
Vol 96 (3) ◽  
Author(s):  
Lijun Bao ◽  
Likun Gu ◽  
Bo Sun ◽  
Wenyang Cai ◽  
Shiwei Zhang ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Tree Species ◽  
High Throughput Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Pcr Analysis ◽  
Forest Park ◽  
Growing Seasons ◽  
Different Seasons ◽  
Pinus Bungeana

ABSTRACT Phyllosphere harbors diverse microorganisms, which influence plant growth and health. In order to understand the extent to which environmental factors affect epiphytic microbial communities, we characterized microbial communities on leaves of three separate tree species present on the college campus, and also present within a forest park over two seasons. Quantitative PCR analysis showed the quantity of 16S rRNA genes was lower in May compared with October, while the abundances of functional genes (nifH and bacterial amoA genes) were extremely high in May. High-throughput sequencing revealed a large variation in the diversity and composition of bacterial and diazotrophic communities over the two seasons, and showed the abundance of functional genera, such as Nocardioides, Bacillus and Zoogloea were significantly elevated in May. In addition, xenobiotic biodegradation pathways of bacterial communities were clearly elevated in May. Network analysis showed the correlations between phyllospheric bacteria in May were more complex than that in October and showed greater negative correlations. These results were consistent in all tree species in this study. This study showed that phyllospheric bacteria varied greatly in different seasons, which implies that different growing seasons should be considered in the exploitation of the interactions between phyllospheric microorganisms and host plants.

scholarly journals Elevated Carbon Dioxide Alters the Structure of Soil Microbial Communities

2012 ◽  
Vol 78 (8) ◽  
pp. 2991-2995 ◽  
Author(s):  
Ye Deng ◽  
Zhili He ◽  
Meiying Xu ◽  
Yujia Qin ◽  
Joy D. Van Nostrand ◽  
...  
Keyword(s):  
Carbon Dioxide ◽  
Microbial Communities ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Soil Microbial ◽  
Composition And Structure ◽  
Pyrosequencing Analysis ◽  
Soil Microbial Community Composition

ABSTRACTPyrosequencing analysis of 16S rRNA genes was used to examine impacts of elevated CO2(eCO2) on soil microbial communities from 12 replicates each from ambient CO2(aCO2) and eCO2settings. The results suggest that the soil microbial community composition and structure significantly altered under conditions of eCO2, which was closely associated with soil and plant properties.

scholarly journals Seasonal dynamics of methane cycling microbial communities in Amazonian floodplain sediments

2020 ◽  
Author(s):  
Júlia B. Gontijo ◽  
Andressa M. Venturini ◽  
Caio A. Yoshiura ◽  
Clovis D. Borges ◽  
José Mauro S. Moura ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Seasonal Dynamics ◽  
Abiotic Factors ◽  
Microbial Community Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sediment Chemistry ◽  
Floodplain Forests ◽  
Variable Environment ◽  
Floodplain Sediments

AbstractThe Amazonian floodplain forests are dynamic ecosystems of great importance for the regional hydrological and biogeochemical cycles and provide a significant contribution to the global carbon balance. Unique geochemical factors may drive the microbial community composition and, consequently, affect CH4 emissions across floodplain areas. Here we provide the first report of the in situ seasonal dynamics of CH4 cycling microbial communities in Amazonian floodplains. We asked how abiotic factors may affect both overall and CH4 cycling microbial communities and further investigated their responses to seasonal changes. We collected sediment samples during wet and dry seasons from three different types of floodplain forests, along with upland forest soil samples, from the Eastern Amazon, Brazil. We used high-resolution sequencing of archaeal and bacterial 16S rRNA genes combined with real-time PCR to quantify Archaea and Bacteria, as well as key functional genes indicative of the methanogenic (methyl coenzyme-M reductase – mcrA) and methanotrophic (particulate methane monooxygenase – pmoA) metabolisms. Methanogens were found to be present in high abundance in floodplain sediments and they seem to resist to dramatic seasonal environmental changes. Methanotrophs known to use different pathways to oxidise CH4 were detected, including anaerobic archaeal and bacterial taxa, indicating that a wide metabolic diversity may be harboured in this highly variable environment. The floodplain environmental variability, which is affected by the river origin, drives not only the sediment chemistry, but also the composition of the microbial communities. The results presented may contribute to the understanding of the current state of CH4 cycling in this region.

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