Effects of shading levels on the composition and co-occurrence patterns of bacterioplankton and epibiotic bacterial communities of Cabomba caroliniana

Abstract. Permafrost thaw ponds and lakes are widespread across the northern landscape and may play a central role in global biogeochemical cycles, yet knowledge about their microbial ecology is limited. We sampled a set of thaw ponds and lakes as well as shallow rock-basin lakes that are located in distinct valleys along a North–South permafrost degradation gradient. We applied high-throughput sequencing of the 16S rRNA gene to determine co-occurrence patterns among bacterial taxa, and then analyzed these results relative to environmental variables to identify factors controlling bacterial community structure. Network analysis was applied to identify possible ecological linkages among the bacterial taxa and with abiotic and biotic variables. The results showed an overall high level of shared taxa among bacterial communities within each valley, however the bacterial co-occurrence patterns were non-random, with evidence of habitat preferences. There were taxonomic differences in bacterial assemblages among the different valleys that were statistically related to dissolved organic carbon concentration, conductivity and phytoplankton biomass. Co-occurrence networks revealed complex interdependencies within the bacterioplankton communities and showed contrasting linkages to environmental conditions among the main bacterial phyla. The thaw pond networks were composed of a limited number of highly connected taxa. This "small world network" property would render the communities more robust to environmental change but vulnerable to the loss of microbial keystone species.

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Elevation rather than season determines the assembly and co-occurrence patterns of soil bacterial communities in forest ecosystems of Mount Gongga

Applied Microbiology and Biotechnology ◽

10.1007/s00253-020-10783-w ◽

2020 ◽

Vol 104 (17) ◽

pp. 7589-7602 ◽

Cited By ~ 2

Author(s):

Bingjian Zhu ◽

Chaonan Li ◽

Junming Wang ◽

Jiabao Li ◽

Xiangzhen Li

Keyword(s):

Bacterial Communities ◽

Forest Ecosystems ◽

Soil Bacterial Communities ◽

Soil Bacterial ◽

Occurrence Patterns

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Compositions and Co-occurrence Patterns of Bacterial Communities Associated With Polymer- and ASP-Flooded Petroleum Reservoir Blocks

Frontiers in Microbiology ◽

10.3389/fmicb.2020.580363 ◽

2020 ◽

Vol 11 ◽

Author(s):

Guoling Ren ◽

Jinlong Wang ◽

Lina Qu ◽

Wei Li ◽

Min Hu ◽

...

Keyword(s):

Oil Recovery ◽

Bacterial Communities ◽

Chemical Properties ◽

Oil Production ◽

Chemical Flooding ◽

Petroleum Reservoir ◽

Promising Alternative ◽

Asp Flooding ◽

Production Wells ◽

Occurrence Patterns

Polymer flooding technology and alkaline-surfactant-polymer (ASP) flooding technology have been widely used in some oil reservoirs. About 50% of remaining oil is trapped, however, in polymer-flooded and ASP-flooded reservoirs. How to further improve oil recovery of these reservoirs after chemical flooding is technically challenging. Microbial enhanced oil recovery (MEOR) technology is a promising alternative technology. However, the bacterial communities in the polymer-flooded and ASP-flooded reservoirs have rarely been investigated. We investigated the distribution and co-occurrence patterns of bacterial communities in ASP-flooded and polymer-flooded oil production wells. We found that Arcobacter and Pseudomonas were dominant both in the polymer-flooded and ASP-flooded production wells. Halomonas accounted for a large amount of the bacterial communities inhabiting in the ASP-flooded blocks, whereas they were hardly detected in the polymer-flooded blocks, and the trends for Acetomicrobium were the opposite. RDA analysis indicated that bacterial communities in ASP-flooded and polymer-flooded oil production wells are closely related to the physical and chemical properties, such as high salinity and strong alkaline, which together accounted for 56.91% of total variance. Co-occurrence network analysis revealed non-random combination patterns of bacterial composition from production wells of ASP-flooded and polymer-flooded blocks, and the ASP-flooded treatment decreased bacterial network complexity, suggesting that the application of ASP flooding technology reduced the tightness of bacterial interactions.

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Co-occurrence patterns in aquatic bacterial communities across changing permafrost landscapes

Biogeosciences ◽

10.5194/bg-13-175-2016 ◽

2016 ◽

Vol 13 (1) ◽

pp. 175-190 ◽

Cited By ~ 31

Author(s):

J. Comte ◽

C. Lovejoy ◽

S. Crevecoeur ◽

W. F. Vincent

Keyword(s):

Bacterial Communities ◽

High Throughput Sequencing ◽

Habitat Preferences ◽

Microbial Consortia ◽

Rrna Gene ◽

Permafrost Degradation ◽

Food Web Structure ◽

Bacterial Phyla ◽

Organic Carbon Concentration ◽

Occurrence Patterns

Abstract. Permafrost thaw ponds and lakes are widespread across the northern landscape and may play a central role in global biogeochemical cycles, yet knowledge about their microbial ecology is limited. We sampled a set of thaw ponds and lakes as well as shallow rock-basin lakes that are located in distinct valleys along a north–south permafrost degradation gradient. We applied high-throughput sequencing of the 16S rRNA gene to determine co-occurrence patterns among bacterial taxa (operational taxonomic units, OTUs), and then analyzed these results relative to environmental variables to identify variables controlling bacterial community structure. Network analysis was applied to identify possible ecological linkages among the bacterial taxa and with abiotic and biotic variables. The results showed an overall high level of shared taxa among bacterial communities within each valley; however, the bacterial co-occurrence patterns were non-random, with evidence of habitat preferences. There were taxonomic differences in bacterial assemblages among the different valleys that were statistically related to dissolved organic carbon concentration, conductivity and phytoplankton biomass. Co-occurrence networks revealed complex interdependencies within the bacterioplankton communities and showed contrasting linkages to environmental conditions among the main bacterial phyla. The thaw pond networks were composed of a limited number of highly connected taxa. This “small world network” property would render the communities more robust to environmental change but vulnerable to the loss of microbial “keystone species”. These highly connected nodes (OTUs) in the network were not merely the numerically dominant taxa, and their loss would alter the organization of microbial consortia and ultimately the food web structure and functioning of these aquatic ecosystems.

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Host species shapes the co-occurrence patterns rather than diversity of stomach bacterial communities in pikas

Applied Microbiology and Biotechnology ◽

10.1007/s00253-017-8254-0 ◽

2017 ◽

Vol 101 (13) ◽

pp. 5519-5529 ◽

Cited By ~ 11

Author(s):

Huan Li ◽

Tongtong Li ◽

Bo Tu ◽

Yongping Kou ◽

Xiangzhen Li

Keyword(s):

Host Species ◽

Bacterial Communities ◽

Occurrence Patterns

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The Formation of Antibiotic Resistance Genes in Bacterial Communities During Garlic Powder Processing

Frontiers in Nutrition ◽

10.3389/fnut.2021.800932 ◽

2021 ◽

Vol 8 ◽

Author(s):

Yanxia Liu ◽

Peng Gao ◽

Yuhao Wu ◽

Xiaorui Wang ◽

Xiaoming Lu ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Bacterial Communities ◽

Powder Processing ◽

Antibiotic Resistance Genes ◽

Garlic Powder ◽

The World ◽

Number Of Microorganisms ◽

Occurrence Patterns ◽

And Control

Chinese garlic powder (GP) is exported to all countries in the world, but the excess of microorganisms is a serious problem that affects export. The number of microorganisms has a serious impact on the pricing of GP. It is very important to detect and control the microorganism in GP. The purpose of this study was to investigate the contamination and drug resistance of microorganisms during the processing of GP. We used metagenomics and Illumina sequencing to study the composition and dynamic distribution of antibiotic resistance genes (ARGs), but also the microbial community in three kinds of garlic products from factory processing. The results showed that a total of 126 ARG genes were detected in all the samples, which belonged to 11 ARG species. With the processing of GP, the expression of ARGs showed a trend to increase at first and then to decrease. Network analysis was used to study the co-occurrence patterns among ARG subtypes and bacterial communities and ARGs.

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Disentangling Archaeal and Bacterial Biogeography and Co-occurrence Networks in Subtropical Mangrove Sediments Under Spartina Alterniflora Invasion

10.21203/rs.3.rs-113333/v1 ◽

2020 ◽

Author(s):

Weidong Chen ◽

Donghui Wen

Keyword(s):

Spartina Alterniflora ◽

Bacterial Communities ◽

Amplicon Sequencing ◽

Mangrove Ecosystem ◽

Microbial Interactions ◽

Rrna Gene ◽

Relative Role ◽

Ecological Processes ◽

Rare Taxa ◽

Occurrence Patterns

Abstract Background: Mangrove ecosystems are vulnerable due to the exotic Spartina alterniflora invasion in China. Large knowledge gaps remain with regard to archaeal and bacterial communities assembly processes and microbial interactions under S. alterniflora invasion. Here, using 16S rRNA gene amplicon sequencing, we investigated the assembly processes and co-occurrence relationships of the archaeal and bacterial communities under S. alterniflora invasion along the coastlines of Fujian province, southeast China.Results: We found that the overall archaeal and bacterial communities were driven predominantly by stochastic processes, and the relative role of stochasticity was stronger for bacteria than archaea. Co-occurrence network analysis showed that the network structure of bacteria was more complex than that of the archaea. Putative keystone taxa often had low relative abundances (conditionally rare taxa), suggesting conditionally rare taxa or low abundances taxa may significantly contribute to network stability. Moreover, we found that S. alterniflora invasion changed the microbial communities assembly and co-occurrence patterns, indicating that S. alterniflora affected the composition and stability of the microbial community.Conclusions: This study provides the first comparison in the biogeography and co-occurrence patterns of both archaea and bacteria in mangrove ecosystem. And this is the first exploration about the effect of S. alterniflora invasion on archaeal and bacterial ecological processes and co-occurrence patterns. Our study considers that the control of S. alterniflora invasion is important for mangrove ecosystem function and service.

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Effects of copper on the composition and diversity of microbial communities in laboratory-scale swine manure composting

Canadian Journal of Microbiology ◽

10.1139/cjm-2017-0622 ◽

2018 ◽

Vol 64 (6) ◽

pp. 409-419 ◽

Cited By ~ 4

Author(s):

Yanan Yin ◽

Jie Gu ◽

Xiaojuan Wang ◽

Xiaxia Tuo ◽

Kaiyu Zhang ◽

...

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

Pathogenic Bacteria ◽

High Throughput Sequencing ◽

Swine Manure ◽

Principal Component ◽

Water Soluble ◽

Soluble Carbohydrates ◽

Occurrence Patterns ◽

Temperature Water

This study investigated the effects of adding copper at 3 treatment levels (0 (control: CK), 200 (low: L), and 2000 (high: H) mg·kg−1 treatments) on the bacterial communities during swine manure composting. The abundances of the bacteria were determined by quantitative PCR and their compositions were evaluated by high-throughput sequencing. The results showed that the abundance of bacteria was inhibited by the H treatment during days 7–35, and principal component analysis clearly separated the H treatment from the CK and L treatments. Actinobacteria, Firmicutes, and Proteobacteria were the dominant bacterial taxa, and a high copper concentration decreased the abundances of bacteria that degrade cellulose and lignin (e.g., class Bacilli and genus Truepera), especially in the mesophilic and thermophilic phases. Moreover, network analysis showed that copper might alter the co-occurrence patterns of bacterial communities by changing the properties of the networks and the keystone taxa, and increase the competition by increasing negative associations between bacteria during composting. Temperature, water-soluble carbohydrates, and copper significantly affected the variations in the bacterial community according to redundancy analysis. The copper content mainly contributed to the bacterial community in the thermophilic and cooling phases, where it had positive relationships with potentially pathogenic bacteria (e.g., Corynebacterium_1 and Acinetobacter).

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