Geographical Distribution of Iron Redox Cycling Bacterial Community in Peatlands: Distinct Assemble Mechanism Across Environmental Gradient

Microbial-mediated iron (Fe) oxidation and reduction greatly contribute to the biogeochemistry and mineralogy of ecosystems. However, knowledge regarding the composition and distribution patterns of iron redox cycling bacteria in peatlands remains limited. Here, using high-throughput sequencing, we compared biogeographic patterns and assemblies of the iron redox cycling bacterial community between soil and water samples obtained from different types of peatland across four regions in Northeast China. A total of 48 phylotypes were identified as potential iron redox bacteria, which had greater than 97% similarity with Fe(II)-oxidizing bacteria (FeOB) and Fe(III)-reducing bacteria (FeRB). Among them, Rhodoferax, Clostridium, Geothrix, Sideroxydans, Geobacter, Desulfovibrio, and Leptothrix could be used as bioindicators in peatlands for characterizing different hydrological conditions and nutrient demands. Across all samples, bacterial communities associated with iron redox cycling were mainly affected by pH, dissolved organic carbon (DOC), and Fe2+. Distance–decay relationship (DDR) analysis indicated that iron redox cycling bacterial communities in soil, but not in water, were highly correlated with geographic distance. Additionally, null model analysis revealed that stochastic processes substituted deterministic processes from minerotrophic fens to ombrotrophic bogs in soils, whereas deterministic processes were dominant in water. Overall, these observations suggest that bacteria involved in iron redox cycling are widespread in diverse habitats and exhibit distinct patterns of distribution and community assembly mechanisms between soil and water in peatlands.

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The Composition and Assembly of Bacterial Communities across the Rhizosphere and Phyllosphere Compartments of Phragmites Australis

Diversity ◽

10.3390/d11060098 ◽

2019 ◽

Vol 11 (6) ◽

pp. 98 ◽

Cited By ~ 5

Author(s):

Qi Zhou ◽

Xiaomin Zhang ◽

Rujia He ◽

Shuren Wang ◽

Congcong Jiao ◽

...

Keyword(s):

Bacterial Community ◽

Phragmites Australis ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Null Model ◽

Rrna Gene ◽

Rare Taxa ◽

Alpha And Beta Diversity ◽

Deterministic Processes ◽

The Difference

The rhizosphere and the phyllosphere represent two different epiphytic compartments of host plant, which are closely related to plant growth, health, and productivity. However, the understanding of the diversity, composition, and assembly of the bacterial communities in different epiphytic microenvironments of large emerged macrophytes has remained elusive, especially the abundant and rare taxa across rhizosphere and phyllosphere communities. In this study, we collected samples of two different epiphytic compartments (rhizosphere and phyllosphere) of Phragmites australis. Both 16S rRNA gene-based high-throughput sequencing and null-model analysis were employed to determine the difference in the composition and assembly of above-mentioned epiphytic bacterial communities. Our results indicated that bacterial communities of rhizosphere exhibited higher diversity and richness than those of phyllosphere. Deterministic processes dominated the assembly of bacterial community in both compartments, and stochastic processes contributed a certain proportion (30.30%) in the assembly of phyllosphere bacterial community. We also found that rare taxa contributed more significantly to the alpha- and beta-diversity of bacterial community than those of abundant taxa. The obtained data are useful for better understanding the bacterial community of different epiphytic compartments of P. australis.

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Local domestication of microbes via cassava beer fermentation

10.7287/peerj.preprints.233 ◽

2014 ◽

Author(s):

Alese Colehour ◽

James F Meadow ◽

Tara J Cepon-Robins ◽

Theresa E Gildner ◽

Melissa A Liebert ◽

...

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Bacterial Communities ◽

Manihot Esculenta ◽

Nutritional Quality ◽

High Throughput Sequencing ◽

Bacterial Community Composition ◽

Ribosomal Gene ◽

Ecuadorian Amazon ◽

Traditional Fermentation

Cassava beer, or chicha, is typically consumed daily by the indigenous Shuar people of the Ecuadorian Amazon. This traditional beverage made from cassava tuber (Manihot esculenta) improves nutritional quality and flavor while extending shelf life in a tropical climate. Bacteria responsible for chicha fermentation could be a source of microbes beneficial to human health, but little is known regarding the microbiology of chicha. We investigated bacterial community composition of chicha batches using Illumina high-throughput sequencing. Fermented chicha samples were collected from seven Shuar households in two neighboring villages in the Morona-Santiago region of Ecuador, and the composition of the bacterial communities within each chicha sample was determined by sequencing a region of the 16S ribosomal gene. Members of the genus Lactobacillus dominated all samples, demonstrating that chicha is a source of organisms related to known probiotics. Significantly greater taxonomic similarity was observed between communities in chicha samples taken within a village than those from different villages. Community composition varied among chicha samples, even those separated by short geographic distances, suggesting that ecological and/or evolutionary processes, including human preference, may be responsible for creating locally adapted and regionally resilient ferments. Our results suggest that traditional fermentation may be a form of domestication that provides endemic beneficial inocula for consumers.

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Differential Impacts of Water Table and Temperature on Bacterial Communities in Pore Water From a Subalpine Peatland, Central China

Frontiers in Microbiology ◽

10.3389/fmicb.2021.649981 ◽

2021 ◽

Vol 12 ◽

Author(s):

Wen Tian ◽

Xing Xiang ◽

Hongmei Wang

Keyword(s):

Amino Acids ◽

Bacterial Community ◽

Pore Water ◽

Water Table ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Acid Methyl Ester ◽

Central China ◽

Utilization Rate ◽

Carbon Utilization

The level of water table and temperature are two environmental variables shaping soil bacterial communities, particularly in peatland ecosystems. However, discerning the specific impact of these two factors on bacterial communities in natural ecosystems is challenging. To address this issue, we collected pore water samples across different months (August and November in 2017 and May 2018) with a gradient of water table changes and temperatures at the Dajiuhu peatland, Central China. The samples were analyzed with 16S rRNA high-throughput sequencing and Biolog EcoMicroplates. Bacterial communities varied in the relative abundances of dominant taxa and harbored exclusive indicator operational taxonomic units across the different months. Despite these differences, bacterial communities showed high similarities in carbon utilization, with preferences for esters (pyruvic acid methyl ester, Tween 40, Tween 80, and D-galactonic acid γ-lactone), amino acids (L-arginine and L-threonine), and amines (phenylethylamine and putrescine). However, rates of carbon utilization (as indicated by average well-color development) and metabolic diversity (McIntosh and Shannon index) in May and August were higher than those in November. Redundancy analysis revealed that the seasonal variations in bacterial communities were significantly impacted by the level of the water table, whereas the temperature had a fundamental role in bacterial carbon utilization rate. Co-occurrence analysis identified Sphingomonas, Mucilaginibacter, Novosphingobium, Lacunisphaera, Herminiimonas, and Bradyrhizobium as keystone species, which may involve in the utilization of organic compounds such as amino acids, phenols, and others. Our findings suggest that bacterial community functions were more stable than their compositions in the context of water table changes. These findings significantly expand our current understanding of the variations of bacterial community structures and metabolic functions in peatland ecosystems in the context of global warming and fluctuation of the water table.

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Local domestication of microbes via cassava beer fermentation

10.7287/peerj.preprints.233v1 ◽

2014 ◽

Author(s):

Alese Colehour ◽

James F Meadow ◽

Tara J Cepon-Robins ◽

Theresa E Gildner ◽

Melissa A Liebert ◽

...

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Bacterial Communities ◽

Manihot Esculenta ◽

Nutritional Quality ◽

High Throughput Sequencing ◽

Bacterial Community Composition ◽

Ribosomal Gene ◽

Ecuadorian Amazon ◽

Traditional Fermentation

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Enzyme additives influence bacterial communities of Medicago sativa silage as determined by Illumina sequencing

10.21203/rs.3.rs-29755/v1 ◽

2020 ◽

Author(s):

Zongfu Hu ◽

Deying Ma ◽

huaxin Niu ◽

Jie Chang ◽

Jianhua Yu ◽

...

Keyword(s):

Lactic Acid ◽

Bacterial Community ◽

High Throughput ◽

Bacterial Communities ◽

Crude Protein ◽

High Throughput Sequencing ◽

Ammonium N ◽

Enzyme Combination ◽

Fermentation Quality ◽

Dominant Bacteria

Abstract This study aimed to evaluate the effects of enzymes (cellulase combined with galactosidase),, and the combination of these enzymes with Lactobacillus plantarum (LP) on bacterial diversity using high-throughput sequencing. Alfalfa forages were treated without or with cellulase + ɑ-galactosidase (CEGA), cellulase + LP (CELP), ɑ-galactosidase + LP (GALP). After 56 days of ensiling, All the treated silages exhibited improved fermentation quality as reflecting by decreased pH, ammonium-N and increased lactic acid levels compared to the control silage. Enzymatic treatment improved nutrients value by increased the level of crude protein and decreased the neutral detergent fibre (NDF) level. Treatment of the silage significantly changed the bacterial community, as determined by the PCoA test. LAB dominated the bacterial community of the treated silage after ensiling. The dominant bacteria from Garciella, Enterococcus, Lactobacillus and Pediococcus in control silage changed to Lactobacillus and Pediococcus in CEGA silage, and Lactobacillus in CELP and GALP silages. Collectively, enzymes and enzyme in combination with inoculants both greatly increased the abundance of LAB, with Enterococcus, Lactobacillus and Pediococcus in enzymes only silge (CEGA) and Lactobacillus in enzyme combination with inoculants silage (CELP and GALP).

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Growing season drives the compositional changes and assembly processes of epiphytic bacterial communities of two submerged macrophytes in Taihu Lake

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa025 ◽

2020 ◽

Vol 96 (4) ◽

Author(s):

Dan He ◽

Lijuan Ren ◽

Qinglong L Wu

Keyword(s):

Stochastic Processes ◽

Bacterial Communities ◽

Taihu Lake ◽

Submerged Macrophytes ◽

Geographic Distance ◽

Null Model ◽

Alpha Diversity ◽

Growing Season ◽

Epiphytic Bacteria ◽

Alpha And Beta Diversity

ABSTRACT Large amounts of epiphytic bacteria live on the leaf surfaces of submerged macrophytes in freshwater lakes. Despite their important roles in affecting host plant's health and biogeochemical cycling, knowledge about epiphytic bacteria assembly is not sufficient. We studied epiphytic bacteria on two cohabiting plant species in Taihu Lake, China. In comparison with plant identity and geographic distance, the plant-growing season played a prominent role in driving alpha and beta diversity (compositional variations) of epiphytic bacterial communities. Phylogeny-based null model analysis revealed that the growing season also drove the relative importance of deterministic versus stochastic processes underlying bacterial community assembly. In May when both plants start growth, the deterministic processes were most prominent, while in months later than June, the stochastic processes’ effects increased substantially. In addition, we found a significant positive relationship between alpha diversity and compositional stochasticity, implying that stochastic processes may have great effects on the maintenance of diversity and functioning of epiphytic bacteria in aquatic ecosystems. In summary, the growing season overwhelmed plant identity and spatial site in shaping epiphytic bacterial communities in Taihu Lake, which may suggest new clues in understanding the dynamics of epiphytic communities and their roles in large shallow lacustrine ecosystems.

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Comparative analysis of biofilm community on different coloured substrata in relation to mussel settlement

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315415002222 ◽

2016 ◽

Vol 97 (1) ◽

pp. 81-89 ◽

Cited By ~ 7

Author(s):

Yi-Feng Li ◽

Xing-Pan Guo ◽

Yu-Ru Chen ◽

De-Wen Ding ◽

Jin-Long Yang

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Current Knowledge ◽

Illumina Miseq ◽

Miseq Sequencing ◽

Significant Difference ◽

The World ◽

Community Variability ◽

Biofilm Community

Mussels are typical macrofouling organisms in the world. In this study, the interaction between the settlement ofMytilus coruscusplantigrades and bacterial community on coloured substrata was determined. Bacterial communities in biofilms developed on seven coloured substrata were analysed by Illumina Miseq sequencing. The mussel settlement response to coloured substrata with no biofilms was also examined.Flavobacteria, AlphaproteobacteriaandGammaproteobacteriawere the first, second and third most dominant groups in seven biofilm samples. The results suggest that the inducing activities of these biofilms on plantigrade settlement varied with coloured substrata and the lowest percentage of settlement was observed on biofilms on the green substratum. High-throughput sequencing showed that bacterial community in biofilms also changed with the substratum colour. No significant difference in the inducing activity on plantigrade settlement was observed between the coloured substrata with no biofilms. Thus, difference in plantigrade settlement response may be correlated to the changes in bacterial community on coloured substrata. This finding extends current knowledge of interaction among mussel settlement and bacterial community variability.

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High throughput sequencing-based analysis of the soil bacterial community structure and functions of Tamarix shrubs in the lower reaches of the Tarim River

PeerJ ◽

10.7717/peerj.12105 ◽

2021 ◽

Vol 9 ◽

pp. e12105

Author(s):

Fangnan Xiao ◽

Yuanyuan Li ◽

Guifang Li ◽

Yaling He ◽

Xinhua Lv ◽

...

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

Metabolic Pathways ◽

Soil Bacteria ◽

High Throughput Sequencing ◽

Soil Bacterial Community ◽

Tarim River ◽

Soil Bacterial Communities ◽

Soil Bacterial ◽

And Function

Tamarix is a dominant species in the Tarim River Basin, the longest inland river in China. Tamarix plays an important role in the ecological restoration of this region. In this study, to investigate the soil bacterial community diversity in Tamarix shrubs, we collected soil samples from the inside and edge of the canopy and the edge of nebkhas and non-nebkhas Tamarix shrubs located near the Yingsu section in the lower reaches of Tarim River. High throughput sequencing technology was employed to discern the composition and function of soil bacterial communities in nebkhas and non-nebkhas Tamarix shrubs. Besides, the physicochemical properties of soil and the spatial distribution characteristics of soil bacteria and their correlation were analyzed. The outcomes of this analysis demonstrated that different parts of Tamarix shrubs had significantly different effects on soil pH, total K (TK), available K (AK), ammonium N (NH4+), and available P (AP) values (P < 0.05), but not on soil moisture (SWC), total salt (TDS), electrical conductivity (EC), organic matter (OM), total N (TN), total P (TP), and nitrate N (NO3−) values. The soil bacterial communities identified in Tamarix shrubs were categorized into two kingdoms, 71 phyla, 161 classes, 345 orders, 473 families, and 702 genera. Halobacterota, unidentified bacteria, and Proteobacteria were found to be dominant phyla. The correlation between the soil physicochemical factors and soil bacterial community was analyzed, and as per the outcomes OM, AK, AP, EC, and NH4+ were found to primarily affect the structure of the soil bacterial community. SWC, TK and pH were positively correlated with each other, but negatively correlated with other soil factors. At the phyla level, a significantly positive correlation was observed between the Halobacterota and AP, OM as well as Bacteroidota and AK (P < 0.01), but a significantly negative correlation was observed between the Chloroflexi and AK, EC (P < 0.01). The PICRUSt software was employed to predict the functional genes. A total of 6,195 KEGG ortholog genes were obtained. The function of soil bacteria was annotated, and six metabolic pathways in level 1, 41 metabolic pathways in level 2, and 307 metabolic pathways in level 3 were enriched, among which the functional gene related to metabolism, genetic information processing, and environmental information processing was found to have the dominant advantage. The results showed that the nebkhas and canopy of Tamarix shrubs had a certain enrichment effect on soil nutrients content, and bacterial abundance and significant effects on the structure and function of the soil bacterial community.

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Bacterial communities in paddy soil and ditch sediment under rice-crab co-culture system

AMB Express ◽

10.1186/s13568-021-01323-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Xu Jiang ◽

Hui Ma ◽

Qing-lei Zhao ◽

Jun Yang ◽

Cai-yun Xin ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Relative Abundance ◽

Paddy Soil ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

High Throughput Sequencing ◽

Available Phosphorus ◽

Uncultured Bacterium ◽

Ditch Sediment

AbstractAs an important form of sustainable agriculture, rice-crab (Eriocheir sinensis) co-culture is rapid developing worldwide. However, the knowledge on the bacterial communities of the different components of the system is limited. In this study, we investigated the bacterial community structure in paddy soil and ditch sediment by using high-throughput sequencing technology. The results showed that compared with the ditch sediment, the content of NH4+-N in paddy soil decreased by 62.31%, and the content of AP (available phosphorus) increased by 172.02% (P < 0.05). The most abundant phyla in paddy soil and ditch sediment were Proteobacteria, Bacteroidetes and Chloroflexi, whose relative abundance was above 65%. Among the dominant genera, the relative abundance of an uncultured bacterium genus of Saprospiraceae and an uncultured bacterium genus of Lentimicrobiaceae in paddy soil was significantly lower than ditch sediment (P < 0.05). Alpha diversity indicated that the bacterial diversity of paddy soil and ditch sediment was similar. The bacterial community structure was affected by the relative abundance of bacteria, not the species of bacteria. Redundancy analysis (RDA) showed that the bacterial communities in paddy soil and ditch sediment were correlated with physicochemical properties. Our findings showed that the bacterial community structure was distinct in paddy soil and ditch sediment under rice-crab co-culture probably due to their different management patterns. These results can provide theoretical support for improving rice-crab co-culture technology.

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Long-term continuously monocropped peanut significantly changed the abundance and composition of soil bacterial communities

PeerJ ◽

10.7717/peerj.9024 ◽

2020 ◽

Vol 8 ◽

pp. e9024

Author(s):

Mingna Chen ◽

Hu Liu ◽

Shanlin Yu ◽

Mian Wang ◽

Lijuan Pan ◽

...

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Abundant Species ◽

Bacterial Populations ◽

Soil Sickness ◽

Community Function ◽

Soil Bacterial Communities ◽

Short And Long Term

Soil sickness is the progressive loss of soil quality due to continuous monocropping. The bacterial populations are critical to sustaining agroecosystems, but their responses to long-term peanut monocropping have not been determined. In this study, based on a previously constructed gradient of continuous monocropped plots, we tracked the detailed feedback responses of soil bacteria to short- and long-term continuous monocropping of four different peanut varieties using high-throughput sequencing techniques. The analyses showed that soil samples from 1- and 2-year monocropped plots were grouped into one class, and samples from the 11- and 12-year plots were grouped into another. Long-term consecutive monocropping could lead to a general loss in bacterial diversity and remarkable changes in bacterial abundance and composition. At the genera level, the dominant genus Bacillus changed in average abundance from 1.49% in short-term monocropping libraries to 2.96% in the long-term libraries. The dominant species Bacillus aryabhattai and Bacillus funiculus and the relatively abundant species Bacillus luciferensis and Bacillus decolorationis all showed increased abundance with long-term monocropping. Additionally, several other taxa at the genus and species level also presented increased abundance with long-term peanut monocropping; however, several taxa showed decreased abundance. Comparing analyses of predicted bacterial community functions showed significant changes at different KEGG pathway levels with long-term peanut monocropping. Combined with our previous study, this study indicated that bacterial communities were obviously influenced by the monocropping period, but less influenced by peanut variety and growth stage. Some bacterial taxa with increased abundance have functions of promoting plant growth or degrading potential soil allelochemicals, and should be closely related with soil remediation and may have potential application to relieve peanut soil sickness. A decrease in diversity and abundance of bacterial communities, especially beneficial communities, and simplification of bacterial community function with long-term peanut monocropping could be the main cause of peanut soil sickness.

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