scholarly journals Microbial Diversity in Water and Sediment of Lake Chaka, an Athalassohaline Lake in Northwestern China

2006 ◽  
Vol 72 (6) ◽  
pp. 3832-3845 ◽  
Author(s):  
Hongchen Jiang ◽  
Hailiang Dong ◽  
Gengxin Zhang ◽  
Bingsong Yu ◽  
Leah R. Chapman ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Lake Water ◽  
Bacterial Community Composition ◽  
Major Change ◽  
Archaeal Community ◽  
Northwest China ◽  
Hypersaline Lake ◽  
Average Water ◽  
Sediment Interface

ABSTRACT We employed culture-dependent and -independent techniques to study microbial diversity in Lake Chaka, a unique hypersaline lake (32.5% salinity) in northwest China. It is situated at 3,214 m above sea level in a dry climate. The average water depth is 2 to 3 cm. Halophilic isolates were obtained from the lake water, and halotolerant isolates were obtained from the shallow sediment. The isolates exhibited resistance to UV and gamma radiation. Microbial abundance in the sediments ranged from 108 cells/g at the water-sediment interface to 107 cells/g at a sediment depth of 42 cm. A major change in the bacterial community composition was observed across the interface. In the lake water, clone sequences affiliated with the Bacteroidetes were the most abundant, whereas in the sediments, sequences related to low G+C gram-positive bacteria were predominant. A similar change was also present in the archaeal community. While all archaeal clone sequences in the lake water belonged to the Halobacteriales, the majority of the sequences in the sediments were related to those previously obtained from methanogenic soils and sediments. The observed changes in the microbial community structure across the water-sediment interface were correlated with a decrease in salinity from the lake water (32.5%) to the sediments (approximately 4%). Across the interface, the redox state also changed from oxic to anoxic and may also have contributed to the observed shift in the microbial community.

scholarly journals Artificial neural network analysis of microbial diversity in the central and southern Adriatic Sea

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Danijela Šantić ◽  
Kasia Piwosz ◽  
Frano Matić ◽  
Ana Vrdoljak Tomaš ◽  
Jasna Arapov ◽  
...  
Keyword(s):  
Neural Network ◽  
Network Analysis ◽  
Bacterial Community ◽  
Microbial Diversity ◽  
Community Composition ◽  
Adriatic Sea ◽  
Bacterial Community Composition ◽  
Environmental Data ◽  
Large Contribution ◽  
Neural Network Analysis

AbstractBacteria are an active and diverse component of pelagic communities. The identification of main factors governing microbial diversity and spatial distribution requires advanced mathematical analyses. Here, the bacterial community composition was analysed, along with a depth profile, in the open Adriatic Sea using amplicon sequencing of bacterial 16S rRNA and the Neural gas algorithm. The performed analysis classified the sample into four best matching units representing heterogenic patterns of the bacterial community composition. The observed parameters were more differentiated by depth than by area, with temperature and identified salinity as important environmental variables. The highest diversity was observed at the deep chlorophyll maximum, while bacterial abundance and production peaked in the upper layers. The most of the identified genera belonged to Proteobacteria, with uncultured AEGEAN-169 and SAR116 lineages being dominant Alphaproteobacteria, and OM60 (NOR5) and SAR86 being dominant Gammaproteobacteria. Marine Synechococcus and Cyanobium-related species were predominant in the shallow layer, while Prochlorococcus MIT 9313 formed a higher portion below 50 m depth. Bacteroidota were represented mostly by uncultured lineages (NS4, NS5 and NS9 marine lineages). In contrast, Actinobacteriota were dominated by a candidatus genus Ca. Actinomarina. A large contribution of Nitrospinae was evident at the deepest investigated layer. Our results document that neural network analysis of environmental data may provide a novel insight into factors affecting picoplankton in the open sea environment.

scholarly journals Soil Bacterial Community Diversity and Composition as Affected by Tillage Intensity Treatments in Corn-Soybean Production Systems

2021 ◽  
Vol 12 (1) ◽  
pp. 157-172
Author(s):  
Shankar G. Shanmugam ◽  
Normie W. Buehring ◽  
Jon D. Prevost ◽  
William L. Kingery
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Community Composition ◽  
Production System ◽  
Soil Microbial Community ◽  
Production Systems ◽  
Bacterial Community Composition ◽  
Soybean Production ◽  
Soil Microbial ◽  
Soil Bacterial

Our understanding on the effects of tillage intensity on the soil microbial community structure and composition in crop production systems are limited. This study evaluated the soil microbial community composition and diversity under different tillage management systems in an effort to identify management practices that effectively support sustainable agriculture. We report results from a three-year study to determine the effects on changes in soil microbial diversity and composition from four tillage intensity treatments and two residue management treatments in a corn-soybean production system using Illumina high-throughput sequencing of 16S rRNA genes. Soil samples were collected from tillage treatments at locations in the Southern Coastal Plain (Verona, Mississippi, USA) and Southern Mississippi River Alluvium (Stoneville, Mississippi, USA) for soil analysis and bacterial community characterization. Our results indicated that different tillage intensity treatments differentially changed the relative abundances of bacterial phyla. The Mantel test of correlations indicated that differences among bacterial community composition were significantly influenced by tillage regime (rM = 0.39, p ≤ 0.0001). Simpson’s reciprocal diversity index indicated greater bacterial diversity with reduction in tillage intensity for each year and study location. For both study sites, differences in tillage intensity had significant influence on the abundance of Proteobacteria. The shift in the soil bacterial community composition under different tillage systems was strongly correlated to changes in labile carbon pool in the system and how it affected the microbial metabolism. This study indicates that soil management through tillage intensity regime had a profound influence on diversity and composition of soil bacterial communities in a corn-soybean production system.

scholarly journals Stochastic Assembly Leads to Alternative Communities with Distinct Functions in a Bioreactor Microbial Community

mBio ◽  
2013 ◽  
Vol 4 (2) ◽  
Author(s):  
Jizhong Zhou ◽  
Wenzong Liu ◽  
Ye Deng ◽  
Yi-Huei Jiang ◽  
Kai Xue ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Diversity ◽  
Microbial Community Structure ◽  
Community Assembly ◽  
Ecosystem Functioning ◽  
Dominant Role ◽  
Microbial Biodiversity ◽  
Stochastic Assembly

ABSTRACTThe processes and mechanisms of community assembly and its relationships to community functioning are central issues in ecology. Both deterministic and stochastic factors play important roles in shaping community composition and structure, but the connection between community assembly and ecosystem functioning remains elusive, especially in microbial communities. Here, we used microbial electrolysis cell reactors as a model system to examine the roles of stochastic assembly in determining microbial community structure and functions. Under identical environmental conditions with the same source community, ecological drift (i.e., initial stochastic colonization) and subsequent biotic interactions created dramatically different communities with little overlap among 14 identical reactors, indicating that stochastic assembly played dominant roles in determining microbial community structure. Neutral community modeling analysis revealed that deterministic factors also played significant roles in shaping microbial community structure in these reactors. Most importantly, the newly formed communities differed substantially in community functions (e.g., H2production), which showed strong linkages to community structure. This study is the first to demonstrate that stochastic assembly plays a dominant role in determining not only community structure but also ecosystem functions. Elucidating the links among community assembly, biodiversity, and ecosystem functioning is critical to understanding ecosystem functioning, biodiversity preservation, and ecosystem management.IMPORTANCEMicroorganisms are the most diverse group of life known on earth. Although it is well documented that microbial natural biodiversity is extremely high, it is not clear why such high diversity is generated and maintained. Numerous studies have established the roles of niche-based deterministic factors (e.g., pH, temperature, and salt) in shaping microbial biodiversity, the importance of stochastic processes in generating microbial biodiversity is rarely appreciated. Moreover, while microorganisms mediate many ecosystem processes, the relationship between microbial diversity and ecosystem functioning remains largely elusive. Using a well-controlled laboratory system, this study provides empirical support for the dominant role of stochastic assembly in creating variations of microbial diversity and the first explicit evidence for the critical role of community assembly in influencing ecosystem functioning. The results presented in this study represent important contributions to the understanding of the mechanisms, especially stochastic processes, involved in shaping microbial biodiversity.

Impacts of invasive plant species on soil biodiversity: a case study of dog-strangling vine (Vincetoxicum rossicum) in a Canadian National Park

2018 ◽  
Vol 98 (4) ◽  
pp. 716-723 ◽  
Author(s):  
Laura N. Bugiel ◽  
Stuart W. Livingstone ◽  
Marney E. Isaac ◽  
Roberta R. Fulthorpe ◽  
Adam R. Martin
Keyword(s):  
Bacterial Community ◽  
Microbial Diversity ◽  
Community Composition ◽  
Invasive Plant ◽  
Bacterial Community Composition ◽  
Anthropogenic Disturbances ◽  
Soil Parameters ◽  
Invasive Plant Species ◽  
Vincetoxicum Rossicum ◽  
Soil Bacterial

Soil microbial diversity is expected to be altered by the establishment of invasive plant species, such as dog-strangling vine (DSV) [Vincetoxicum rossicum (Apocynaceae)]. However, in urban ecosystems where DSV invasion is high, there is little research evaluating the impacts of DSV and other anthropogenic disturbances on microbial diversity. Our study was based in Rouge National Urban Park, Canada, where we used terminal restriction fragment length polymorphism data to evaluate (i) if DSV has a detectable impact on soil bacterial community composition and (ii) if these impacts occur independently of other anthropogenic change or soil characteristics. Variation in soil bacterial communities was greatly reduced in DSV-invaded sites vs. less-invaded sites. The degree of DSV invasion independently explained 23.8% of variation in bacterial community composition: a value similar to the explanatory power of proximity to roadways (which explained 22.6% of the variation in community composition), and considerably greater than soil parameters (pH, moisture, carbon, and nitrogen concentrations) which explained only between 6.0% and 10.0% of variation in bacterial community composition. Our findings indicate that DSV influences soil bacterial community composition independent of other anthropogenic disturbances and soil parameters, with potential impacts on multiple facets of plant–soil interactions and plant invasion dynamics.

scholarly journals Variation of Bacterial and Archaeal Community Structures in a Full-Scale Constructed Wetlands for Wastewater Treatment

Archaea ◽  
2018 ◽  
Vol 2018 ◽  
pp. 1-12 ◽  
Author(s):  
Xiu-lu Lang ◽  
Xiang Chen ◽  
Ai-ling Xu ◽  
Zhi-wen Song ◽  
Xin Wang ◽  
...  
Keyword(s):  
Microbial Community ◽  
Constructed Wetlands ◽  
Relative Abundance ◽  
Constructed Wetland ◽  
Free Surface Flow ◽  
Archaeal Community ◽  
Illumina Miseq ◽  
Surface Flow ◽  
Community Structures ◽  
Soil And Water

Microorganisms play important roles in the reduction of organic and inorganic pollutants in constructed wetlands used for the treatment of wastewater. However, the diversity and structure of microbial community in constructed wetland system remain poorly known. In this study, the Illumina MiSeq Sequencing of 16S rDNA was used to analyze the bacterial and archaeal microbial community structures of soil and water in a free surface flow constructed wetland, and the differences of bacterial communities and archaeal compositions between soil and water were compared. The results showed that the Proteobacteria were the dominant bacteria, making up 35.38%~48.66% relative abundance. Euryarchaeotic were the absolute dominant archaea in the influent sample with the relative abundance of 93.29%, while Thaumarchaeota showed dominance in the other three samples, making up 50.58%~75.70%. The relative abundances of different species showed great changes in bacteria and archaea, and the number of dominant species in bacteria was much higher than that in archaea. Compared to archaea, the community compositions of bacteria were more abundant and the changes were more significant. Meanwhile, bacteria and archaea had large differences in compositions between water and soil. The microbial richness in water was significantly higher than that in soil. Simultaneously, soil had a significant enrichment effect on some microbial flora.

scholarly journals Abundance and Microbial Diversity from Surface to Deep Water Layers Over the Rio Grande Rise, South Atlantic

2021 ◽  
Author(s):  
Juliana Correa Neiva Ferreira ◽  
Natascha M. Bergo ◽  
Pedro M. Tura ◽  
Mateus Gustavo Chuqui ◽  
Frederico P. Brandini ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Rio Grande ◽  
South Atlantic ◽  
Water Masses ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
List Type ◽  
Tropical Water ◽  
Southwestern Atlantic Ocean

AbstractMarine microbes control the flux of matter and energy essential for life in the oceans. Until now, the distribution and diversity of planktonic microorganisms above Fe-Mn crusts has received relatively little attention. Future mining\dredging of these minerals is predicted to affect microbial diversity and functioning in the deep sea. Here, we studied the ecology of planktonic microbes among pelagic environments of an Fe-Mn deposit region, at Rio Grande Rise, Southwestern Atlantic Ocean. We investigated microbial community composition using high-throughput sequencing of 16S rRNA genes and their abundance estimated by flow cytometry. Our results showed that the majority of picoplanktonic was found in epi- and mesopelagic waters, corresponding to the Tropical Water and South Atlantic Central Water. Bacterial and archaeal groups related to phototrophy, heterotrophy and chemosynthesis, such as Synechococcales, Sar11 (Proteobacteria) and Nitrosopumilales (Thaumarchaeota) were the main representatives of the pelagic microbial community. Additionally, we detected abundant assemblages involved in biodegradation of marine organic matter and iron oxidation at deep waters, i.e., Pseudoalteromonas and Alteromonas. No differences were observed in microbial community alpha diversity. However, we detected differences in community structure between water masses, suggesting that changes in an environmental setting (i.e. nutrient availability or circulation) play a significant role in structuring the pelagic zones, also affecting the meso- and bathypelagic microbiome.HighlightsRio Grande Rise pelagic microbiomePicoplankton carbon biomass partitioning through pelagic zonesUnique SAR11 Clade I oligotype in the shallowest Tropical WaterHigher number of shared oligotypes between deepest water massesNitrogen, carbon and sulfur may be important contributors for the pelagic microbiome

scholarly journals Effect of Pyroligneous Acid on the Microbial Community Composition and Plant Growth-Promoting Bacteria (PGPB) in Soils

Soil Systems ◽  
2022 ◽  
Vol 6 (1) ◽  
pp. 10
Author(s):  
Anithadevi Kenday Sivaram ◽  
Logeshwaran Panneerselvan ◽  
Kannappar Mukunthan ◽  
Mallavarapu Megharaj
Keyword(s):  
Microbial Community ◽  
Plant Growth ◽  
Microbial Diversity ◽  
Growth And Yield ◽  
Rrna Gene ◽  
Plant Growth Promoting Bacteria ◽  
Microbial Composition ◽  
Pyroligneous Acid ◽  
Plant Growth Promoting ◽  
Growth Promoting

Pyroligneous acid (PA) is often used in agriculture as a plant growth and yield enhancer. However, the influence of PA application on soil microorganisms is not often studied. Therefore, in this study, we investigated the effect of PA (0.01–5% w/w in soil) on the microbial diversity in two different soils. At the end of eight weeks of incubation, soil microbial community dynamics were determined by Illumina-MiSeq sequencing of 16S rRNA gene amplicons. The microbial composition differed between the lower (0.01% and 0.1%) and the higher (1% and 5%) concentration in both PA spiked soils. The lower concentration of PA resulted in higher microbial diversity and dehydrogenase activity (DHA) compared to the un-spiked control and the soil spiked with high PA concentrations. Interestingly, PA-induced plant growth-promoting bacterial (PGPB) genera include Bradyrhizobium, Azospirillum, Pseudomonas, Mesorhizobium, Rhizobium, Herbaspiriluum, Acetobacter, Beijerinckia, and Nitrosomonas at lower concentrations. Additionally, the PICRUSt functional analysis revealed the predominance of metabolism as the functional module’s primary component in both soils spiked with 0.01% and 0.1% PA. Overall, the results elucidated that PA application in soil at lower concentrations promoted soil DHA and microbial enrichment, particularly the PGPB genera, and thus have great implications for improving soil health.

scholarly journals STRUKTUR KOMUNITAS MIKROBA TANAH DAN IMPLIKASINYA DALAM MEWUJUDKAN SISTEM PERTANIAN BERKELANJUTAN

el–Hayah ◽  
2012 ◽  
Vol 1 (4) ◽  
Author(s):  
Prihastuti Prihastuti
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Microbial Communities ◽  
Soil Microbial Community ◽  
Soil Microbial Communities ◽  
Organic Soil ◽  
Plant Type ◽  
Soil Microbial Community Structure ◽  
Soil Microbial ◽  
Wide Range

<p>Soils are made up of organic and an organic material. The organic soil component contains all the living creatures in the soil and the dead ones in various stages of decomposition.  Biological activity in soil helps to recycle nutrients, decompose organic matter making nutrient available for plant uptake, stabilize humus, and form soil particles.<br />The extent of the diversity of microbial in soil is seen to be critical to the maintenance of soil health and quality, as a wide range of microbial is involved in important soil functions.  That ecologically managed soils have a greater quantity and diversity of soil microbial. The two main drivers of soil microbial community structure, i.e., plant type and soil type, are thought to exert their function in a complex manner. The fact that in some situations the soil and in others the plant type is the key factor determining soil microbial diversity is related to their complexity of the microbial interactions in soil, including interactions between microbial and soil and microbial and plants. <br />The basic premise of organic soil stewardship is that all plant nutrients are present in the soil by maintaining a biologically active soil environment. The diversity of microbial communities has on ecological function and resilience to disturbances in soil ecosystems. Relationships are often observed between the extent of microbial diversity in soil, soil and plant quality and ecosystem sustainability. Agricultural management can be directed toward maximizing the quality of the soil microbial community in terms of disease suppression, if it is possible to shift soil microbial communities.</p><p>Keywords: structure, microbial, implication, sustainable agriculture<br /><br /></p>

scholarly journals New insights into the influence of plant and microbial diversity on denitrification rates in a salt marsh

2020 ◽  
Author(s):  
Olivia U. Mason ◽  
Patrick Chanton ◽  
Loren N. Knobbe ◽  
Julian Zaugg ◽  
Behzad Mortazavi
Keyword(s):  
Microbial Community ◽  
Salt Marsh ◽  
Microbial Diversity ◽  
Ecosystem Functions ◽  
Juncus Roemerianus ◽  
Rrna Gene ◽  
Metabolic Potential ◽  
Marsh Vegetation ◽  
Core Microbiome ◽  
N Removal

AbstractCoastal salt marshes are some of the most productive ecosystems on Earth, providing numerous services such as soil carbon storage, flood protection and nutrient filtering, several of which are mediated by the sediment microbiome associated with marsh vegetation. Here, nutrient filtering (nitrate removal through denitrification) was examined by determining microbial community structure (16S rRNA gene iTag sequencing), diversity, denitrification rates and metabolic potential (assembled metagenomic sequences) in collocated patches of Spartina alterniflora (Spartina) and Juncus roemerianus (Juncus) sediments. The iTag data showed that diversity and richness in Spartina and Juncus sediment microbial communities were highly similar. However, microbial community evenness differed significantly, with the most even communities observed in Juncus sediments. Further, denitrification rates were significantly higher in Juncus compared to Spartina, suggesting oscillations in microbial abundances and in particular the core microbiome identified herein, along with plant diversity influence marsh nitrogen (N) removal. Amplicon and assembled metagenome sequences pointed to a potentially important, yet unappreciated Planctomycetes role in N removal in the salt marsh. Thus, perturbations, such as sea-level rise, that can alter marsh vegetation distribution could impact microbial diversity and may ultimately influence the ecologically important ecosystem functions the marsh sediment microbiome provides.

scholarly journals Evaluation of DNA Extraction Methods of Mule Dung

2019 ◽  
Vol 4 (3) ◽  
pp. 170-174
Author(s):  
Rajesh Kumar Vaid ◽  
Taruna Anand ◽  
Priyanka Batra ◽  
Ram Avtar Legha ◽  
Bhupendra Nath Tripathi
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Dna Isolation ◽  
Community Analysis ◽  
Extraction Methods ◽  
Microbial Community Analysis ◽  
Animal Dung ◽  
Microbial Community Analyses ◽  
Dna Extraction Methods ◽  
Selection Of

DNA isolation is a critical step in microbial community analysis of animal dung. DNA isolation from mule dung is challenging due to microbial diversity, composition and chemical nature of mule dung. Therefore, selection of an appropriate DNA isolation method is important to analyse the complete microbial diversity. In the current study, we evaluated the DNA isolation from mule dung samples (n=11) using QiAmp Mini stool kit as per manufacturer’s procedure with modifications. The results suggest that modifications in proprietary column based method improved the DNA quality and quantity suitable for mule dung microbial community analyses.

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