Variation of bacterial communities along the vertical gradient in Lake Issyk Kul, Kyrgyzstan

AbstractIn this study, we explored the diversity and community composition of bacteria along a vertical gradient in Lake Issyk Kul, Kyrgyzstan, one of the largest and deepest brackish lakes in in the world. We identified 4904 bacterial ASVs based on analysis of 16S rRNA gene sequences and determined significant changes in the composition responding mainly to the variables depth and salinity. A higher abundance of Proteobacteria and Bacteroidetes was observed in the surface waters and the lake tributaries. Cyanobacteria were more abundant in the deep chlorophyll maximum (28.5 to 128 m), while Planctomycetes and Chloroflexi were dominant at depths between 128 to 600 m. According to our machine learning analysis used for identifying the most critical environmental factors, depth and temperature revealed the strongest effect on members of Proteobacteria, Planctomycetes, and Chloroflexi, while oxygen is associated with the variations in Cyanobacteria. Also, a notable increase in alpha diversity estimations was observed with increasing water depth. This work evidences significant differences in the structure of bacterial communities along the depth gradient in deep, transparent lake ecosystems. Notably, there is a dominance of Planctomycetes and Chloroflexi in the deepest layers, which can only be seen in a few other lakes with similar characteristics as Lake Issyk Kul and raises questions about their ecological role.

Download Full-text

Nutrients Drive the Structures of Bacterial Communities in Sediments and Surface Waters in the River-Lake System of Poyang Lake

Water ◽

10.3390/w11050930 ◽

2019 ◽

Vol 11 (5) ◽

pp. 930 ◽

Cited By ~ 3

Author(s):

Ze Ren ◽

Xiaodong Qu ◽

Wenqi Peng ◽

Yang Yu ◽

Min Zhang

Keyword(s):

Surface Waters ◽

Bacterial Communities ◽

Poyang Lake ◽

Current Knowledge ◽

Interactive System ◽

Lake Ecosystem ◽

Rrna Gene ◽

Nitrogen And Phosphorus ◽

Lake Ecosystems ◽

Lake System

Lake and its inflow rivers compose a highly linked river-lake system, within which sediment and water are also closely connected. However, our understanding of this linked and interactive system remains unclear. In this study, we examined bacterial communities in the sediments and surface waters in Poyang Lake and its five tributaries. Bacterial communities were determined while using high-throughput 16S rRNA gene sequencing. The results showed significant differences of bacterial communities between sediments and surface waters, as well as between Poyang lake and its tributaries, suggesting that the river-lake system of Poyang Lake provides diverse and distinct habitats for bacterial communities, including lake water, lake sediment, river water, and river sediment. These biomes harbor distinct bacterial assemblages. Sediments harbor more diverse bacterial taxa than surface waters, but the bacterial communities in surface waters were more different across this river-lake system than those in sediments. In this eutrophic river-lake ecosystem, nitrogen and phosphorus were important drivers in sediment bacterial communities. Nitrogen, phosphorus, and dissolved organic carbon, as well as their stoichiometric ratios affected bacterial communities in surface waters. Moreover, network analysis revealed that the bacterial communities in surface waters were more vulnerable to various disturbances than in sediments, due to lower alpha diversity, high complexity of network, and a small number of key taxa (module hubs and connectors). Nutrient variables had strong influences on individual operational taxonomic units (OTUs) in the network, especially in bacterial network in surface waters. Different groups of taxa responded differently to nutrients, with some modules being more susceptible to nutrient variations. This study increased our current knowledge of linked river-lake ecosystems and provided valuable understanding for effective management and protection of these ecosystems by revealing bacterial communities in sediments and surface waters in Poyang Lake and its tributaries, as well as their responses to nutrients variation.

Download Full-text

Functional profiling of bacterial communities in Lake Tuz using 16S rRNA gene sequences

Biotechnology & Biotechnological Equipment ◽

10.1080/13102818.2020.1840437 ◽

2020 ◽

Vol 35 (1) ◽

pp. 1-10

Author(s):

Habeebat Adekilekun Oyewusi ◽

Roswanira Abdul Wahab ◽

Mohamed Faraj Edbeib ◽

Mohd Azrul Naim Mohamad ◽

Azzmer Azzar Abdul Hamid ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Bacterial Communities ◽

Rrna Gene ◽

Gene Sequences ◽

16S Rrna Gene Sequences ◽

Functional Profiling

Download Full-text

Gut microbiota composition is associated with narcolepsy type 1

Neurology Neuroimmunology & Neuroinflammation ◽

10.1212/nxi.0000000000000896 ◽

2020 ◽

Vol 7 (6) ◽

pp. e896

Author(s):

Alexandre Lecomte ◽

Lucie Barateau ◽

Pedro Pereira ◽

Lars Paulin ◽

Petri Auvinen ◽

...

Keyword(s):

Community Structure ◽

Gut Microbiota ◽

Bacterial Communities ◽

Beta Diversity ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Differential Abundance ◽

Alpha And Beta Diversity

ObjectiveTo test the hypothesis that narcolepsy type 1 (NT1) is related to the gut microbiota, we compared the microbiota bacterial communities of patients with NT1 and control subjects.MethodsThirty-five patients with NT1 (51.43% women, mean age 38.29 ± 19.98 years) and 41 controls (57.14% women, mean age 36.14 ± 12.68 years) were included. Stool samples were collected, and the fecal microbiota bacterial communities were compared between patients and controls using the well-standardized 16S rRNA gene amplicon sequencing approach. We studied alpha and beta diversity and differential abundance analysis between patients and controls, and between subgroups of patients with NT1.ResultsWe found no between-group differences for alpha diversity, but we discovered in NT1 a link with NT1 disease duration. We highlighted differences in the global bacterial community structure as assessed by beta diversity metrics even after adjustments for potential confounders as body mass index (BMI), often increased in NT1. Our results revealed differential abundance of several operational taxonomic units within Bacteroidetes, Bacteroides, and Flavonifractor between patients and controls, but not after adjusting for BMI.ConclusionWe provide evidence of gut microbial community structure alterations in NT1. However, further larger and longitudinal multiomics studies are required to replicate and elucidate the relationship between the gut microbiota, immunity dysregulation and NT1.

Download Full-text

Niche specificity and functional diversity of the bacterial communities associated with Ginkgo biloba and Panax quinquefolius

Scientific Reports ◽

10.1038/s41598-021-90309-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Hanan R. Shehata ◽

Subramanyam Ragupathy ◽

Thomas A. Henry ◽

Steven G. Newmaster

Keyword(s):

Functional Diversity ◽

Ginkgo Biloba ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Alpha Diversity ◽

Panax Quinquefolius ◽

Tissue Type ◽

Rrna Gene ◽

Associated Bacteria ◽

Kegg Pathways

AbstractPlant-associated bacteria can establish mutualistic relationships with plants to support plant health. Plant tissues represent heterogeneous niches with distinct characteristics and may thus host distinct microbial populations. The objectives of this study are to investigate the bacterial communities associated with two medicinally and commercially important plant species; Ginkgo biloba and Panax quinquefolius using high Throughput Sequencing (HTS) of 16S rRNA gene, and to evaluate the extent of heterogeneity in bacterial communities associated with different plant niches. Alpha diversity showed that number of operational taxonomic units (OTUs) varied significantly by tissue type. Beta diversity revealed that the composition of bacterial communities varied between tissue types. In Ginkgo biloba and Panax quinquefolius, 13% and 49% of OTUs, respectively, were ubiquitous in leaf, stem and root. Proteobacteria, Bacteroidetes, Actinobacteria and Acidobacteria were the most abundant phyla in Ginkgo biloba while Proteobacteria, Bacteroidetes, Actinobacteria, Plantomycetes and Acidobacteria were the most abundant phyla in Panax quinquefolius. Functional prediction of these bacterial communities using MicrobiomeAnalyst revealed 5843 and 6251 KEGG orthologs in Ginkgo biloba and Panax quinquefolius, respectively. A number of these KEGG pathways were predicted at significantly different levels between tissues. These findings demonstrate the heterogeneity, niche specificity and functional diversity of plant-associated bacteria.

Download Full-text

Response of Root-Associated Bacterial Communities to Different Degrees of Soft Rot Damage in Amorphophallus konjac Under a Robinia pseudoacacia Plantation

Frontiers in Microbiology ◽

10.3389/fmicb.2021.652758 ◽

2021 ◽

Vol 12 ◽

Author(s):

Fei He

Keyword(s):

Community Composition ◽

Bacterial Communities ◽

Disease Incidence ◽

Robinia Pseudoacacia ◽

Alpha Diversity ◽

Soft Rot ◽

Rrna Gene ◽

Illumina Hiseq ◽

Amorphophallus Konjac ◽

Damage Degree

Bacterial soft rot is a destructive disease that restricts the development of the konjac (Amorphophallus konjac K. Koch ex N.E.Br) industry. The objective of this study was to investigate how soft rot disease affects bacterial communities associated with the roots of konjac plants growing under a pure Robinia pseudoacacia plantation. Three sampling sites affected by different degrees of soft rot damage were selected based on the disease incidence [0%, non-diseased (ND); 4.2%, moderately diseased (MD); and 18.6%, highly diseased (HD)]. The variation in soil and root bacterial diversity and community composition among the sampling sites was determined by Illumina HiSeq sequencing of the V3–V4 hypervariable regions of the bacterial 16S rRNA gene. The results showed that the contents of soil organic matter and available nutrients (N, P, and K) increased with increasing damage degree, whereas higher damage degree resulted in lower soil pH and enzymatic activity (sucrase, urease, catalase, and polyphenol oxidase). The composition of root-associated bacterial communities differed among the three sampling sites. Proteobacteria was the most dominant bacterial phylum in all soil and root samples. Pseudomonas, Bacillus, Rhizobium, and Streptomyces were the most abundant in all samples from the ND sites, whereas Pectobacterium carotovorum and Serratia were predominant in the samples from the MD and HD sites. The abundance and alpha diversity of root-associated bacteria were significantly higher (p < 0.05) in the ND sites than in the diseased sites. The results suggested pronounced differences in the abundance, alpha diversity, and community composition of bacteria associated with the roots of konjac plants affected by different degrees of soft rot damage. Such differences in bacterial community structure were related to dynamic changes in soil variables, especially soil available potassium content, sucrase activity, and urease activity. Analysis of the dominant root-associated bacterial taxa offers an approach to predict the damage degree due to soft rot in konjac and provides evidence for the prevention of this soil-borne disease via microecological regulation.

Download Full-text

Diversity and Functionality of Culturable Endophytic Bacterial Communities in Chickpea Plants

Plants ◽

10.3390/plants8020042 ◽

2019 ◽

Vol 8 (2) ◽

pp. 42 ◽

Cited By ~ 13

Author(s):

Clarisse Brígido ◽

Sakshi Singh ◽

Esther Menéndez ◽

Maria Tavares ◽

Bernard Glick ◽

...

Keyword(s):

Plant Growth ◽

Bacterial Communities ◽

Endophytic Bacteria ◽

Rrna Gene ◽

16S Rrna Gene Sequences ◽

Mn Toxicity ◽

Rhizobial Inoculation ◽

Plant Growth Promoting ◽

Growth Promoting ◽

Different Soils

The aims of this study were to isolate, identify and characterize culturable endophytic bacteria from chickpea (Cicer arietinum L.) roots grown in different soils. In addition, the effects of rhizobial inoculation, soil and stress on the functionality of those culturable endophytic bacterial communities were also investigated. Phylogenetic analysis based on partial 16S rRNA gene sequences revealed that the endophytic bacteria isolated in this work belong to the phyla Proteobacteria, Firmicutes and Actinobacteria, with Enterobacter and Pseudomonas being the most frequently observed genera. Production of indoleacetic acid and ammonia were the most widespread plant growth-promoting features, while antifungal activity was relatively rare among the isolates. Despite the fact that the majority of bacterial endophytes were salt- and Mn-tolerant, the isolates obtained from soil with Mn toxicity were generally more Mn-tolerant than those obtained from the same soil amended with dolomitic limestone. Several associations between an isolate’s genus and specific plant growth-promoting mechanisms were observed. The data suggest that soil strongly impacts the Mn tolerance of endophytic bacterial communities present in chickpea roots while rhizobial inoculation induces significant changes in terms of isolates’ plant growth-promoting abilities. In addition, this study also revealed chickpea-associated endophytic bacteria that could be exploited as sources with potential application in agriculture.

Download Full-text

Bacterial communities of Beijing surface waters as revealed by 454 pyrosequencing of the 16S rRNA gene

Environmental Science and Pollution Research ◽

10.1007/s11356-015-4534-3 ◽

2015 ◽

Vol 22 (16) ◽

pp. 12605-12614 ◽

Cited By ~ 14

Author(s):

Yu-Mei Wei ◽

Jing-Qi Wang ◽

Ting-Ting Liu ◽

Wei-Wen Kong ◽

Nan Chen ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Surface Waters ◽

Bacterial Communities ◽

454 Pyrosequencing ◽

Rrna Gene ◽

The 16S Rrna Gene

Download Full-text

Unveiling of Novel Radiations within Trichodesmium Cluster by hetR Gene Sequence Analysis

Applied and Environmental Microbiology ◽

10.1128/aem.71.1.190-196.2005 ◽

2005 ◽

Vol 71 (1) ◽

pp. 190-196 ◽

Cited By ~ 27

Author(s):

Pernilla Lundgren ◽

Sven Janson ◽

Sara Jonasson ◽

Alon Singer ◽

Birgitta Bergman

Keyword(s):

Surface Waters ◽

Gene Sequence ◽

Phylogenetic Analyses ◽

Rrna Gene ◽

Gene Sequences ◽

16S Rrna Gene Sequences ◽

Phylogenetic Affiliation ◽

Gene Sequence Analysis ◽

Subtropical Oceans ◽

Cyanobacterial Genus

ABSTRACT The filamentous nonheterocystous cyanobacterial genus Katagnymene is a common diazotrophic component of tropical and subtropical oceans. To assess the phylogenetic affiliation of this taxon, two partial 16S rRNA gene sequences and 25 partial hetR gene sequences originating from the genera Katagnymene and Trichodesmium collected from open, surface waters of the Atlantic, Indian, and Pacific oceans were compared. Single trichomes or colonies were identified morphologically by using light microscopy and then used directly as templates in hetR PCR analyses. In addition, three cultured strains, identified as Katagnymene pelagica, Katagnymene spiralis, and Trichodesmium sp., were examined. The data show that the genus Katagnymene is in the Trichodesmium cluster and that K. pelagica Lemmermann and K. spiralis Lemmermann are most likely one species, despite their different morphologies. Phylogenetic analyses also unveiled four distinct clusters in the Trichodesmium cluster, including one novel cluster. Our findings emphasize the conclusion that known morphological traits used to differentiate marine nonheterocystous cyanobacteria at the genus and species levels correlate poorly with genetic data, and a revision is therefore suggested.

Download Full-text

Distinct Ectomycorrhizospheres Share Similar Bacterial Communities as Revealed by Pyrosequencing-Based Analysis of 16S rRNA Genes

Applied and Environmental Microbiology ◽

10.1128/aem.06742-11 ◽

2012 ◽

Vol 78 (8) ◽

pp. 3020-3024 ◽

Cited By ~ 45

Author(s):

S. Uroz ◽

P. Oger ◽

E. Morin ◽

P. Frey-Klett

Keyword(s):

16S Rrna ◽

Bacterial Communities ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

16S Rrna Gene Sequences ◽

Content Type ◽

Scleroderma Citrinum ◽

The 16S Rrna Gene ◽

Soil Habitat

ABSTRACTAnalysis of the 16S rRNA gene sequences generated fromXerocomus pruinatusandScleroderma citrinumectomycorrhizospheres revealed that similar bacterial communities inhabited the two ectomycorrhizospheres in terms of phyla and genera, with an enrichment of theBurkholderiagenus. Compared to the bulk soil habitat, ectomycorrhizospheres hosted significantly moreAlpha-,Beta-, andGammaproteobacteria.

Download Full-text

Unravelling the composition of soil belowground microbial community before sowing transgenic cotton

Plant Soil and Environment ◽

10.17221/523/2017-pse ◽

2017 ◽

Vol 63 (No. 11) ◽

pp. 512-518

Author(s):

Vital Lourdes ◽

Narvaez Jose A ◽

Cruz Maria Antonia ◽

Ortiz Eyra L ◽

Sanchez Eric ◽

...

Keyword(s):

Bacterial Communities ◽

Chemical Properties ◽

Alpha Diversity ◽

Soil Samples ◽

Bulk Soil ◽

Personal Genome ◽

Transgenic Crop ◽

Rrna Gene ◽

Sequencing Analysis ◽

Ion Torrent Pgm

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.

Download Full-text