scholarly journals Network Analysis Reveals Seasonal Patterns of Bacterial Community Networks in Lake Taihu under Aquaculture Conditions

Water ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 1868 ◽  
Author(s):  
Lin ◽  
Zhao ◽  
Zeng ◽  
Cao ◽  
Jiao
Keyword(s):  
Network Analysis ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Lake Taihu ◽  
Bacterial Species ◽  
Community Networks ◽  
Seasonal Patterns ◽  
Community Interactions ◽  
Important Species ◽  
Bacterial Phyla

Bacterial communities play essential roles in multiple ecological processes, such as primary production and nutrient recycling in aquatic systems. However, although the composition, diversity and function of bacterial communities have been well studied, little is known about the interactions and co-occurrence characteristics of these communities, let alone their seasonal patterns. To investigate the seasonal variations of bacterial community interactions, we collected water samples from four seasons in Lake Taihu and applied network analysis to reveal bacterial community interactions. Bacterial community networks were non-random in structure, and interactions among bacterial taxa in the networks varied markedly in different seasons. The autumnal bacterial network was the largest and most complex among obtained networks, whereas the spring correlation network was the simplest, having no module hubs or connectors. The important species of the networks were the dominant bacterial phyla/classes (e.g., Alphaproteobacteria and Bacteroidetes), although their relative abundance varied among seasons. The relationships between species and measured environmental variables changed over seasons; fewer environmental factors were correlated with bacterial species in the spring bacterial network, while we observed a greater number of species-environment correlations in the winter network. Our study highlights the seasonal differences in bacterial community interactions and expands our understanding of freshwater microbial ecology in systems affected by aquaculture.

Comparative analysis of the total and active bacterial communities in the surface sediment of Lake Taihu

2020 ◽  
Vol 96 (5) ◽  
Author(s):  
Tong-tong Liu ◽  
Hong Yang
Keyword(s):  
Bacterial Community ◽  
Surface Sediment ◽  
Bacterial Communities ◽  
Surface Sediments ◽  
Lake Taihu ◽  
Dynamic Changes ◽  
Dna And Rna ◽  
Close Relationship ◽  
Total Bacterial Community ◽  
Quantitative Results

ABSTRACT Bacterial communities play crucial roles in the biogeochemical cycle of the surface sediments of freshwater lakes, but previous studies on bacterial community changes in this habitat have mostly been based on the total bacterial community (DNA level), while an exploration of the active microbiota at the RNA level has been lacking. Herein, we analysed the bacterial communities in the surface sediments of Lake Taihu at the DNA and RNA levels. Using MiSeq sequencing and real-time quantification, we found that the sequencing and quantitative results obtained at the RNA level compared with the DNA level were more accurate in responding to the spatiotemporal dynamic changes of the bacterial community. Although both sequencing methods indicated that Proteobacteria, Chloroflexi, Acidobacteria, Nitrospirae, Bacteroidetes and Actinobacteria were the dominant phyla, the co-occurrence network at the RNA level could better reflect the close relationship between microorganisms in the surface sediment. Additionally, further analysis showed that Prochlorococcus and Microcystis were the most relevant and dominant genera of Cyanobacteria in the total and active bacterial communities, respectively; our results also demonstrated that the analysis of Cyanobacteria-related groups at the RNA level was more ‘informative’.

scholarly journals Effect of Bacillus mesonae H20-5 Treatment on Rhizospheric Bacterial Community of Tomato Plants under Salinity Stress

2021 ◽  
Vol 37 (6) ◽  
pp. 662-672
Author(s):  
Shin Ae Lee ◽  
Hyeon Su Kim ◽  
Mee Kyung Sang ◽  
Jaekyeong Song ◽  
Hang-Yeon Weon
Keyword(s):  
Bacterial Community ◽  
Plant Growth ◽  
Soil Salinity ◽  
Bacterial Communities ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Plant Growth Promoting Bacteria ◽  
Tomato Plants ◽  
Rhizosphere Soils ◽  
Salinity Levels

Plant growth-promoting bacteria improve plant growth under abiotic stress conditions. However, their effects on microbial succession in the rhizosphere are poorly understood. In this study, the inoculants of Bacillus mesonae strain H20-5 were administered to tomato plants grown in soils with different salinity levels (EC of 2, 4, and 6 dS/m). The bacterial communities in the bulk and rhizosphere soils were examined 14 days after H20-5 treatment using Illumina MiSeq sequencing of the bacterial 16S rRNA gene. Although the abundance of H20-5 rapidly decreased in the bulk and rhizosphere soils, a shift in the bacterial community was observed following H20-5 treatment. The variation in bacterial communities due to H20-5 treatment was higher in the rhizosphere than in the bulk soils. Additionally, the bacterial species richness and diversity were greater in the H20-5 treated rhizosphere than in the control. The composition and structure of the bacterial communities varied with soil salinity levels, and those in the H20-5 treated rhizosphere soil were clustered. The members of Actinobacteria genera, including Kineosporia, Virgisporangium, Actinoplanes, Gaiella, Blastococcus, and Solirubrobacter, were enriched in the H20-5 treated rhizosphere soils. The microbial co-occurrence network of the bacterial community in the H20-5 treated rhizosphere soils had more modules and keystone taxa compared to the control. These findings revealed that the strain H20-5 induced systemic tolerance in tomato plants and influenced the diversity, composition, structure, and network of bacterial communities. The bacterial community in the H20-5 treated rhizosphere soils also appeared to be relatively stable to soil salinity changes.

scholarly journals Uterine and vaginal bacterial community diversity prior to artificial insemination between pregnant and nonpregnant postpartum cows1

2019 ◽  
Vol 97 (10) ◽  
pp. 4298-4304 ◽  
Author(s):  
Taylor B Ault ◽  
Brooke A Clemmons ◽  
Sydney T Reese ◽  
Felipe G Dantas ◽  
Gessica A Franco ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Artificial Insemination ◽  
Bacterial Communities ◽  
Bacterial Species ◽  
Beef Cows ◽  
Community Diversity ◽  
Rrna Gene ◽  
Bacterial Community Diversity ◽  
Hypervariable Regions ◽  
Time Of Breeding

Abstract The present study evaluated the bovine vaginal and uterine bacterial community diversity and its relationship to fertility. Postpartum beef cows (n = 68) were synchronized beginning on day −21 and ending with timed artificial insemination (TAI) on day 0. Pregnancy was diagnosed 30 d after TAI. Uterine and vaginal flushes were collected on day −21, −9, and −2 for bacterial DNA extraction to sequence the V1 to V3 hypervariable regions of the 16S rRNA gene. Results indicated a decrease in the number of bacterial species over time in the uterus of resulting pregnant and nonpregnant beef cows (P < 0.0001). Principal coordinate analyses (PCoA) depicted clustering of samples, indicating closely related bacterial communities, by day in the uterus and vagina (P < 0.0001). At day −2, uterine samples from nonpregnant and pregnant animals clustered separately (P < 0.0001), with nonpregnant animal samples clustering tightly together. Overall, the current study suggests the shift in the reproductive bacterial communities’ diversity and phylogenetic relationship leading up to the time of breeding may contribute to successful pregnancy establishment.

scholarly journals Soil Water Contents Control the Responses of Dissolved Nitrogen Pools and Bacterial Communities to Freeze-Thaw in Temperate Soils

2020 ◽  
Vol 2020 ◽  
pp. 1-10
Author(s):  
Nan Jiang ◽  
Yinghua Juan ◽  
Lulu Tian ◽  
Xiaodong Chen ◽  
Wentao Sun ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Soil Water ◽  
Community Composition ◽  
Bacterial Communities ◽  
N Mineralization ◽  
Bacterial Species ◽  
Bacterial Community Composition ◽  
N Immobilization ◽  
Freeze Thaw ◽  
Dissolved Nitrogen

Background. Freeze-thaw influences soil-dissolved nitrogen (N) pools due to variations in bacterial communities in temperate regions. The availability of soil water is important to soil biogeochemical cycles under frozen conditions. However, it is unclear how soil water content (SWC) mediates the effects of freeze-thaw on soil-dissolved N pools and bacterial communities. Method. In this study, freeze-thaw microcosms were incubated at three levels of SWC, including 10% (air-dried soils), 15% (natural SWC), and 30% (wet soils). In addition to measuring soil-dissolved N pools, variations in bacterial communities were examined using high-throughput sequencing. Results and Conclusions. Total dissolved N (TDN), NO3--N, NH4+-N, microbial biomass N (MBN), and net N mineralization rate (NNMR) were significantly influenced by SWC, freeze-thaw, and their interaction (NH4+-N excluded). N immobilization was inhibited under both low and high SWC, which was accompanied by varied bacterial community composition. However, only higher SWC substantially modified the freeze-thaw effects on the soil-dissolved N pools, characterized by a decrease in N mineralization (especially for the content of NO3--N and NNMR) and an increase in N immobilization (MBN). These scenarios could be significantly correlated to variations in bacterial community composition based on redundancy analysis, especially by species belonging to Bacteroidetes, Nitrospirae, Alphaproteobacteria, Gemmatimonadetes, and Verrucomicrobia (Spearman’s correlations). In conclusion, bacterial species passed through biotic (bacterial species) and abiotic filters (soil N pools) in response to freeze-thaw under varied SWC.

scholarly journals Impact of long-term industrial contamination on the bacterial communities in urban river sediments

2020 ◽  
Author(s):  
lei zhang ◽  
Demei Tu ◽  
Xingchen Li ◽  
Wenxuan Lu ◽  
Jing Li
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Industrial Pollution ◽  
River Sediments ◽  
Urban River ◽  
Bacterial Phyla ◽  
Different Types

Abstract Background: The contamination of the aquatic environment of urban rivers with industrial wastewater has affected the abiotic conditions and biological activities of the trophic levels of the ecosystem, particularly sediments. However, most current research about microorganism in urban aquatic environments has focused on indicator bacteria related to feces and organic pollution. Meanwhile, they ignored the interactions among microorganisms. To deeply understand the impact of industrial contamination on microbial community, we study the bacterial community structure and diversity in river sediments under the influence of different types of industrial pollution by Illumina MiSeq high-throughput sequencing technology and conduct a more detailed analysis of microbial community structure through co-occurrence networks.Results: Although the composition of dominant bacterial phyla in different sediment samples was similar, their relative abundance was different. These dominant bacterial phyla showed significant differences in different types of industrial contaminated sediment. In addition, redundancy analysis indicated that the structure of the bacterial community in river sediments was influenced by a variety of environmental factors. TN, TP, TOC and metals (Cu, Zn and Cd) were the most important driving factors that determined the bacterial community in urban river sediments (P <0.01). According to PICRUSt analysis, the bacterial communities in different locations had similar overall functional profiles. It is worth noting that the 15 functional genes related to xenobiotics biodegradation and metabolism were the most abundant in the same location. The non-random assembly patterns of bacterial composition in different types of industrially polluted sediments were determined by a co-occurrence network. Environmental conditions resulting from different industrial pollutants may play an important role in determining their co-occurrence patterns of these bacterial taxa. Among them, the bacterial taxa involved in carbon and nitrogen cycles in module I were relatively abundant, and the bacterial taxa in module II were involved in the repair of metal pollution.Conclusions: Our data indicate that long-term potential interactions between different types of industrial pollution and taxa collectively affect the structure of the bacterial community in urban river sediments.

scholarly journals Phyllosphere Bacterial Community of Floating Macrophytes in Paddy Soil Environments as Revealed by Illumina High-Throughput Sequencing

2014 ◽  
Vol 81 (2) ◽  
pp. 522-532 ◽  
Author(s):  
Wan-Ying Xie ◽  
Jian-Qiang Su ◽  
Yong-Guan Zhu
Keyword(s):  
Bacterial Community ◽  
Paddy Soil ◽  
Bacterial Communities ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Core Microbiome ◽  
Content Type ◽  
Soil Ecosystems ◽  
Α Diversity ◽  
Floating Macrophytes

ABSTRACTThe phyllosphere of floating macrophytes in paddy soil ecosystems, a unique habitat, may support large microbial communities but remains largely unknown. We tookWolffia australianaas a representative floating plant and investigated its phyllosphere bacterial community and the underlying driving forces of community modulation in paddy soil ecosystems using Illumina HiSeq 2000 platform-based 16S rRNA gene sequence analysis. The results showed that the phyllosphere ofW. australianaharbored considerably rich communities of bacteria, withProteobacteriaandBacteroidetesas the predominant phyla. The core microbiome in the phyllosphere contained genera such asAcidovorax,Asticcacaulis,Methylibium, andMethylophilus. Complexity of the phyllosphere bacterial communities in terms of class number and α-diversity was reduced compared to those in corresponding water and soil. Furthermore, the bacterial communities exhibited structures significantly different from those in water and soil. These findings and the following redundancy analysis (RDA) suggest that species sorting played an important role in the recruitment of bacterial species in the phyllosphere. The compositional structures of the phyllosphere bacterial communities were modulated predominantly by water physicochemical properties, while the initial soil bacterial communities had limited impact. Taken together, the findings from this study reveal the diversity and uniqueness of the phyllosphere bacterial communities associated with the floating macrophytes in paddy soil environments.

scholarly journals Understanding the Linkage between Elevation and the Activated-Sludge Bacterial Community along a 3,600-Meter Elevation Gradient in China

2015 ◽  
Vol 81 (19) ◽  
pp. 6567-6576 ◽  
Author(s):  
Lihua Niu ◽  
Yi Li ◽  
Peifang Wang ◽  
Wenlong Zhang ◽  
Chao Wang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Communities ◽  
Elevation Gradient ◽  
Ammonia Nitrogen ◽  
Phosphorus Concentration ◽  
Total Phosphorus Concentration ◽  
Content Type ◽  
Bacterial Phyla ◽  
Operational Variables

ABSTRACTTo understand the relationship between elevation and bacterial communities in wastewater treatment plants (WWTPs), bacterial communities in 21 municipal WWTPs across China, located 9 to 3,660 m above sea level (masl), were investigated by 454 pyrosequencing. A threshold for the association of elevation with bacterial community richness and evenness was observed at approximately 1,200 masl. At lower elevations, both richness and evenness were not significantly associated with elevation. At higher elevations, significant declines with increased elevations were observed for community richness and evenness. The declining evenness trend at the phylum level was reflected by distinct trends in relative abundance for individual bacterial phyla.Betaproteobacteria,Bacteroidetes, andFirmicutesdisplayed significant increases, while most other phyla showed declines. Spearman correlation analysis indicated that the community richness and evenness at high elevations were more correlated with elevation than with any other single environmental variable. Redundancy analysis indicated that the contribution of elevation to community composition variances increased from 3% at lower elevations to 11% at higher elevations whereas the community composition variance at higher elevations remained much more explained by operational variables (39.2%) than by elevation. The influent total phosphorus concentration, food/microorganism ratio, and treatment process were the three shared dominant contributors to the community composition variance across the whole elevation gradient, followed by effluent ammonia nitrogen and temperature at higher elevations.

scholarly journals Variation of Microbial Communities in Aquatic Sediments under Long-Term Exposure to Decabromodiphenyl Ether and UVA Irradiation

2019 ◽  
Vol 11 (14) ◽  
pp. 3773 ◽  
Author(s):  
Yi-Tang Chang ◽  
Hsi-Ling Chou ◽  
Hui Li ◽  
Stephen Boyd
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Species ◽  
Community Diversity ◽  
High Dose ◽  
Decabromodiphenyl Ether ◽  
Uva Irradiation ◽  
Different Types ◽  
Bde 209

Abiotic components create different types of environmental stress on bacterial communities in aquatic ecosystems. In this study, the long-term exposure to various abiotic factors, namely a high-dose of the toxic chemical decabromodiphenyl ether (BDE-209), continuous UVA irradiation, and different types of sediment, were evaluated in order to assess their influence on the bacterial community. The dominant bacterial community in a single stress situation, i.e., exposure to BDE-209 include members of Comamonadaceae, members of Xanthomonadaceae, a Pseudomonas sp. and a Hydrogenophaga sp. Such bacteria are capable of biodegrading polybrominated diphenyl ethers (PBDEs). When multiple environmental stresses were present, Acidobacteria bacterium and a Terrimonas sp. were predominant, which equipped the population with multiple physiological characteristics that made it capable of both PBDE biodegradation and resistance to UVA irradiation. Methloversatilis sp. and Flavisolibacter sp. were identified as representative genera in this population that were radioresistant. In addition to the above, sediment heterogeneity is also able to alter bacterial community diversity. In total, seventeen species of bacteria were identified in the microcosms containing more clay particles and higher levels of soil organic matter (SOM). This means that these communities are more diverse than in microcosms that contained more sand particles and a lower SOM, which were found to have only twelve identifiable bacterial species. This is the first report to evaluate how changes in bacterial communities in aquatic sediment are affected by the presence of multiple variable environmental factors at the same time.

scholarly journals Bacterial community response to species overrepresentation or omission is strongly influenced by life in spatially structured habitats

2021 ◽  
Author(s):  
Hannah Kleyer ◽  
Robin Tecon ◽  
Dani Or
Keyword(s):  
Bacterial Community ◽  
Species Composition ◽  
Community Composition ◽  
Bacterial Communities ◽  
Liquid Culture ◽  
Interspecific Interactions ◽  
Bacterial Species ◽  
Human Gut ◽  
Natural Habitats ◽  
Bacterial Interactions

AbstractVariations in type and strength of interspecific interactions in natural bacterial communities (e.g., synergistic to inhibitory) affect species composition and community functioning. The extent of interspecific interactions is often modulated by environmental factors that constrain diffusion pathways and cell mobility and limit community spatial arrangement. We studied how spatially structured habitats affect interspecific interactions and influence the resulting bacterial community composition. We used a bacterial community made of 11 well-characterized species that grew in porous habitats (comprised of glass beads) under controlled hydration conditions or in liquid habitats. We manipulated the initial community composition by overrepresenting or removing selected members, and observed community composition over time. Life in porous media reduced the number and strength of interspecific interactions compared to mixed liquid culture, likely due to spatial niche partitioning in porous habitats. The community converged to similar species composition irrespective of the initial species mix, however, the dominant bacterial species was markedly different between liquid culture and structured porous habitats. Moreover, differences in water saturation levels of the porous medium affected community assembly highlighting the need to account for habitat structure and physical conditions to better understand and interpret assembly of bacterial communities. We point at the modulation of bacterial interactions due to spatial structuring as a potential mechanism for promoting community stability and species coexistence, as observed in various natural environments such as soil or human gut.ImportanceBacteria live as complex multispecies communities essential for healthy and functioning ecosystems ranging from soil to the human gut. The bacterial species that form these communities can have positive or negative impact on each other, promoting or inhibiting each other’s growth. Yet, the factors controlling the balance of such interactions in nature, and how these influence the community, are not fully understood. Here, we show that bacterial interactions are modified by life in spatially structured bacterial habitats. These conditions exert important control over the resulting bacterial community regardless of initial species composition. The study demonstrates limitations of inferences from bacterial communities grown in liquid culture relative to behaviour in structured natural habitats such as soil.

scholarly journals Aquatic Macrophytes and Local Factors Drive Bacterial Community Distribution and Interactions in a Riparian Zone of Lake Taihu

Water ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 432
Author(s):  
Yuanjiao LYU ◽  
Rui Huang ◽  
Jin Zeng ◽  
Qinglong L. Wu
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Aquatic Macrophytes ◽  
Riparian Zone ◽  
Bacterial Community Composition ◽  
Freshwater Ecosystems ◽  
Riparian Zones ◽  
Network Structures ◽  
Bacterial Phyla ◽  
Local Factors

Aquatic macrophytes rhizosphere are biogeochemical cycling hotspots in freshwater ecosystems. However, little is known regarding the effect of aquatic macrophytes on bacterial community and interactions in the riparian zones. We investigated the bacterial community composition and network structures along a gradient of the riparian zone as follows: The supralittoral and eulittoral zones with Phragmites australis, the eulittoral and infralittoral zones without P. australi. The bacterial communities in the four zones differed significantly based on taxonomic dissimilarity, but the two zones with P. australis exhibited phylogenetic closeness of the bacterial communities. The characteristics of the bacterial networks, such as connectivity, modularity, and topological roles of OTUs, were totally different between the P. australis and non-P. australis zones. Some bacterial phyla enriched in the P. australis zones were found to be putative keystone taxa in the networks, which might be involved in the regulation of bacterial interactions and plant growth. Moreover, the hydrological regime and particle size were shown to be determinants of the bacterial community and network structures in the riparian zones. In summary, our results show that the role of P. australis and local factors are crucial for constructing bacterial community and interactions in the riparian zones of lakes.

Sign in / Sign up

Export Citation Format

Share Document