Global Trends of Benthic Bacterial Diversity and Community Composition Along Organic Enrichment Gradients of Salmon Farms

The analysis of benthic bacterial community structure has emerged as a powerful alternative to traditional microscopy-based taxonomic approaches to monitor aquaculture disturbance in coastal environments. However, local bacterial diversity and community composition vary with season, biogeographic region, hydrology, sediment texture, and aquafarm-specific parameters. Therefore, without an understanding of the inherent variation contained within community complexes, bacterial diversity surveys conducted at individual farms, countries, or specific seasons may not be able to infer global universal pictures of bacterial community diversity and composition at different degrees of aquaculture disturbance. We have analyzed environmental DNA (eDNA) metabarcodes (V3–V4 region of the hypervariable SSU rRNA gene) of 138 samples of different farms located in different major salmon-producing countries. For these samples, we identified universal bacterial core taxa that indicate high, moderate, and low aquaculture impact, regardless of sampling season, sampled country, seafloor substrate type, or local farming and environmental conditions. We also discuss bacterial taxon groups that are specific for individual local conditions. We then link the metabolic properties of the identified bacterial taxon groups to benthic processes, which provides a better understanding of universal benthic ecosystem function(ing) of coastal aquaculture sites. Our results may further guide the continuing development of a practical and generic bacterial eDNA-based environmental monitoring approach.

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Assessment of microbial community diversity in lakes of İğneada floodplain forest by metabarcoding approach

AQUATIC RESEARCH ◽

10.3153/ar21025 ◽

2021 ◽

Vol 4 (4) ◽

pp. 304-312

Author(s):

E. Gözde Özbayram ◽

brahim Halil Miraloğlu ◽

Bahar İnce

Keyword(s):

Bacterial Community ◽

Bacterial Diversity ◽

High Throughput Sequencing ◽

Floodplain Forest ◽

Community Diversity ◽

Rrna Gene ◽

Community Patterns ◽

Biotechnological Potential ◽

Sequencing Platform ◽

The Family

This paper aims to contribute to the understanding of bacterial community patterns of the lakes of İğneada Floodplain Forest by metabarcoding approach. Within this scope, surface water samples were collected from three lakes located in the area namely Mert Lake, Hamam Lake, and Saka Lake, and the bacterial diversity was assessed by a high throughput sequencing of the 16S rRNA gene. Chao1 richness and Shannon diversity were higher in Saka Lake indicated a more diverse bacterial community. Proteobacteria was by far the most abundant phyla in all lakes. Although Bacteroidetes and Actinobacteria also dominated the community, their abundances differed in each lake. While the family Burkholderiaceae represented 25% of the bacterial community in Saka Lake, the abundances were 9% and 4% in Hamam Lake and Mert Lake, respectively. This study is one of the first investigations specifically focused on the bacterial communities in three lakes of İğneada Floodplain by next-generation sequencing platform and gave a prescreening of the bacterial diversity. Further studies are required to determine the biotechnological potential of this unique habitat.

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Comparison of Respiratory Microbiome Disruption Indices to Predict VAP and VAE risk at LTACH Admission

Infection Control and Hospital Epidemiology ◽

10.1017/ice.2020.711 ◽

2020 ◽

Vol 41 (S1) ◽

pp. s179-s180

Author(s):

Erik Clarke ◽

Kathleen None Chiotos ◽

James Harrigan ◽

Ebbing Lautenbach ◽

Emily Reesey ◽

...

Keyword(s):

Critical Illness ◽

Bacterial Community ◽

16S Rrna ◽

Respiratory Tract ◽

Predictive Performance ◽

Community Diversity ◽

Rrna Gene ◽

Sequence Variant ◽

Antibiotic Exposure ◽

Shannon Diversity

Background: Healthcare exposure results in significant microbiome disruption, particularly in the setting of critical illness, which may contribute to risk for healthcare-associated infections (HAIs). Patients admitted to long-term acute-care hospitals (LTACHs) have extensive prior healthcare exposure and critical illness; significant microbiome disruption has been previously documented among LTACH patients. We compared the predictive value of 3 respiratory tract microbiome disruption indices—bacterial community diversity, dominance, and absolute abundance—as they relate to risk for ventilator-associated pneumonia (VAP) and adverse ventilator-associated events (VAE), which commonly complicate LTACH care. Methods: We enrolled 83 subjects on admission to an academic LTACH for ventilator weaning and performed longitudinal sampling of endotracheal aspirates, followed by 16S rRNA gene sequencing (Illumina HiSeq), bacterial community profiling (QIIME2) for diversity, and 16S rRNA quantitative PCR (qPCR) for total bacterial abundance. Statistical analyses were performed with R and Stan software. Mixed-effects models were fit to relate the admission MDIs to subsequent clinically diagnosed VAP and VAE. Results: Of the 83 patients, 19 had been diagnosed with pneumonia during the 14 days prior to LTACH admission (ie, “recent past VAP”); 23 additional patients were receiving antibiotics consistent with empiric VAP therapy within 48 hours of admission (ie, “empiric VAP therapy”); and 41 patients had no evidence of VAP at admission (ie, “no suspected VAP”). We detected no statistically significant differences in admission Shannon diversity, maximum amplicon sequence variant (ASV)–level proportional abundance, or 16S qPCR across the variables of interest. In isolation, all 3 admission microbiome disruption indices showed poor predictive performance, though Shannon diversity performed better than maximum ASV abundance. Predictive models that combined (1) bacterial diversity or abundance with (2) recent prior VAP diagnosis and (3) concurrent antibiotic exposure best predicted 14-day VAP (type S error < 0.05) and 30-day VAP (type S error < 0.003). In this cohort, VAE risk was paradoxically associated with higher admission Shannon diversity and lower admission maximum ASV abundance. Conclusions: In isolation, respiratory tract microbiome disruption indices obtained at LTACH admission showed poor predictive performance for subsequent VAP and VAE. But diversity and abundance models incorporating recent VAP history and admission antibiotic exposure performed well predicting 14-day and 30-day VAP.Disclosures: NoneFunding: None

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Effects of Simulated Nitrogen Deposition on the Bacterial Community of Urban Green Spaces

Applied Sciences ◽

10.3390/app11030918 ◽

2021 ◽

Vol 11 (3) ◽

pp. 918

Author(s):

Lingzi Mo ◽

Augusto Zanella ◽

Xiaohua Chen ◽

Bin Peng ◽

Jiahui Lin ◽

...

Keyword(s):

Bacterial Community ◽

Bacterial Diversity ◽

Negative Impact ◽

Bacterial Community Composition ◽

N Deposition ◽

Soil Bacterial Community ◽

Rrna Gene ◽

Soil Dna ◽

Urban Green ◽

Soil Bacterial

Continuing nitrogen (N) deposition has a wide-ranging impact on terrestrial ecosystems. To test the hypothesis that, under N deposition, bacterial communities could suffer a negative impact, and in a relatively short timeframe, an experiment was carried out for a year in an urban area featuring a cover of Bermuda grass (Cynodon dactylon) and simulating environmental N deposition. NH4NO3 was added as external N source, with four dosages (N0 = 0 kg N ha−2 y−1, N1 = 50 kg N ha−2 y−1, N2 = 100 kg N ha−2 y−1, N3 = 150 kg N ha−2 y−1). We analyzed the bacterial community composition after soil DNA extraction through the pyrosequencing of the 16S rRNA gene amplicons. N deposition resulted in soil bacterial community changes at a clear dosage-dependent rate. Soil bacterial diversity and evenness showed a clear trend of time-dependent decline under repeated N application. Ammonium nitrogen enrichment, either directly or in relation to pH decrease, resulted in the main environmental factor related to the shift of taxa proportions within the urban green space soil bacterial community and qualified as a putative important driver of bacterial diversity abatement. Such an impact on soil life induced by N deposition may pose a serious threat to urban soil ecosystem stability and surrounding areas.

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Interaction between typical sulfonamides and bacterial diversity in drinking water

Journal of Water and Health ◽

10.2166/wh.2018.210 ◽

2018 ◽

Vol 16 (6) ◽

pp. 914-920 ◽

Cited By ~ 2

Author(s):

Qing Wu ◽

Shuqun Li ◽

Xiaofei Zhao ◽

Xinhua Zhao

Keyword(s):

Drinking Water ◽

Community Structure ◽

Microbial Community ◽

Bacterial Community ◽

Bacterial Diversity ◽

Microbial Community Structure ◽

Antibiotic Use ◽

Community Diversity ◽

Wide Range ◽

Growth Of Bacteria

Abstract The abuse of antibiotics is becoming more serious as antibiotic use has increased. The sulfa antibiotics, sulfamerazine (SM1) and sulfamethoxazole (SMZ), are frequently detected in a wide range of environments. The interaction between SM1/SMZ and bacterial diversity in drinking water was investigated in this study. The results showed that after treatment with SM1 or SMZ at four different concentrations, the microbial community structure of the drinking water changed statistically significantly compared to the blank sample. At the genus level, the proportions of the different bacteria in drinking water may affect the degradation of the SM1/SMZ. The growth of bacteria in drinking water can be inhibited after the addition of SM1/SMZ, and bacterial community diversity in drinking water declined in this study. Furthermore, the resistance gene sul2 was induced by SM1 in the drinking water.

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Rhizobacterial communities of five co-occurring desert halophytes

PeerJ ◽

10.7717/peerj.5508 ◽

2018 ◽

Vol 6 ◽

pp. e5508 ◽

Cited By ~ 3

Author(s):

Yan Li ◽

Yan Kong ◽

Dexiong Teng ◽

Xueni Zhang ◽

Xuemin He ◽

...

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Plant Species ◽

Bacterial Communities ◽

Bacterial Community Composition ◽

Community Diversity ◽

Species Identity ◽

Halostachys Caspica ◽

Lycium Ruthenicum ◽

Limonium Gmelinii

BackgroundRecently, researches have begun to investigate the microbial communities associated with halophytes. Both rhizobacterial community composition and the environmental drivers of community assembly have been addressed. However, few studies have explored the structure of rhizobacterial communities associated with halophytic plants that are co-occurring in arid, salinized areas.MethodsFive halophytes were selected for study: these co-occurred in saline soils in the Ebinur Lake Nature Reserve, located at the western margin of the Gurbantunggut Desert of Northwestern China. Halophyte-associated bacterial communities were sampled, and the bacterial 16S rDNA V3–V4 region amplified and sequenced using the Illumina Miseq platform. The bacterial community diversity and structure were compared between the rhizosphere and bulk soils, as well as among the rhizosphere samples. The effects of plant species identity and soil properties on the bacterial communities were also analyzed.ResultsSignificant differences were observed between the rhizosphere and bulk soil bacterial communities. Diversity was higher in the rhizosphere than in the bulk soils. Abundant taxonomic groups (from phylum to genus) in the rhizosphere were much more diverse than in bulk soils. Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Planctomycetes were the most abundant phyla in the rhizosphere, while Proteobacteria and Firmicutes were common in bulk soils. Overall, the bacterial community composition were not significantly differentiated between the bulk soils of the five plants, but community diversity and structure differed significantly in the rhizosphere. The diversity ofHalostachys caspica,Halocnemum strobilaceumandKalidium foliatumassociated bacterial communities was lower than that ofLimonium gmeliniiandLycium ruthenicumcommunities. Furthermore, the composition of the bacterial communities ofHalostachys caspicaandHalocnemum strobilaceumwas very different from those ofLimonium gmeliniiandLycium ruthenicum. The diversity and community structure were influenced by soil EC, pH and nutrient content (TOC, SOM, TON and AP); of these, the effects of EC on bacterial community composition were less important than those of soil nutrients.DiscussionHalophytic plant species played an important role in shaping associated rhizosphere bacterial communities. When salinity levels were constant, soil nutrients emerged as key factors structuring bacterial communities, while EC played only a minor role. Pairwise differences among the rhizobacterial communities associated with different plant species were not significant, despite some evidence of differentiation. Further studies involving more halophyte species, and individuals per species, are necessary to elucidate plant species identity effects on the rhizosphere for co-occurring halophytes.

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Correlation of Breed, Growth Performance, and Rumen Microbiota in Two Rustic Cattle Breeds Reared Under Different Conditions

Frontiers in Microbiology ◽

10.3389/fmicb.2021.652031 ◽

2021 ◽

Vol 12 ◽

Author(s):

Matteo Daghio ◽

Francesca Ciucci ◽

Arianna Buccioni ◽

Alice Cappucci ◽

Laura Casarosa ◽

...

Keyword(s):

Bacterial Community ◽

Growth Performance ◽

Community Composition ◽

Lipid Composition ◽

High Throughput Sequencing ◽

Bacterial Community Composition ◽

Daily Weight Gain ◽

Rrna Gene ◽

Rumen Microbiota ◽

Cattle Breeds

The use of rustic cattle is desirable to face challenges brought on by climate change. Maremmana (MA) and Aubrac (AU) are rustic cattle breeds that can be successfully used for sustainable production. In this study, correlations between two rearing systems (feedlot and grazing) and the rumen microbiota, the lipid composition of rumen liquor (RL), and the growth performance of MA and AU steers were investigated. Bacterial community composition was characterized by high-throughput sequencing of 16S rRNA gene amplicons, and the RL lipid composition was determined by measuring fatty acid (FA) and the dimethyl acetal profiles. The main factor influencing bacterial community composition was the cattle breed. Some bacterial groups were positively correlated to average daily weight gain for the two breeds (i.e., Rikenellaceae RC9 gut group, Fibrobacter and Succiniclasticum in the rumen of MA steers, and Succinivibrionaceae UCG-002 in the rumen of AU steers); despite this, animal performance appeared to be influenced by short chain FAs production pathways and by the presence of H2 sinks that divert the H2 to processes alternative to the methanogenesis.

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Fungal and Bacterial Diversity Patterns of Two Diversity Levels Retrieved From a Late Decaying Fagus sylvatica Under Two Temperature Regimes

Frontiers in Microbiology ◽

10.3389/fmicb.2020.548793 ◽

2021 ◽

Vol 11 ◽

Author(s):

Sarah Muszynski ◽

Florian Maurer ◽

Sina Henjes ◽

Marcus A. Horn ◽

Matthias Noll

Keyword(s):

Species Richness ◽

Bacterial Community ◽

Mass Loss ◽

Community Composition ◽

Fagus Sylvatica ◽

Temperature Regime ◽

Community Diversity ◽

Interaction Patterns ◽

Temperature Regimes ◽

Natural Diversity

Environmental fluctuations are a common occurrence in an ecosystem, which have an impact on organismic diversity and associated ecosystem services. The aim of this study was to investigate how a natural and a species richness-reduced wood decaying community diversity were capable of decomposing Fagus sylvatica dead wood under a constant and a fluctuating temperature regime. Therefore, microcosms with both diversity levels (natural and species richness-reduced) were prepared and incubated for 8 weeks under both temperature regimes. Relative wood mass loss, wood pH, carbon dioxide, and methane emissions, as well as fungal and bacterial community compositions in terms of Simpson‘s diversity, richness and evenness were investigated. Community interaction patterns and co-occurrence networks were calculated. Community composition was affected by temperature regime and natural diversity caused significantly higher mass loss than richness-reduced diversity. In contrast, richness-reduced diversity increased wood pH. The bacterial community composition was less affected by richness reduction and temperature regimes than the fungal community composition. Microbial interaction patterns showed more mutual exclusions in richness-reduced compared to natural diversity as the reduction mainly reduced abundant fungal species and disintegrated previous interaction patterns. Microbial communities reassembled in richness-reduced diversity with a focus on nitrate reducing and dinitrogen-fixing bacteria as connectors in the network, indicating their high relevance to reestablish ecosystem functions. Therefore, a stochastic richness reduction was followed by functional trait based reassembly to recover previous ecosystem productivity.

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Successional trajectory of bacterial communities in soil are shaped by plant-driven changes during secondary succession

Scientific Reports ◽

10.1038/s41598-020-66638-x ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Mayank Krishna ◽

Shruti Gupta ◽

Manuel Delgado – Baquerizo ◽

Elly Morriën ◽

Satish Chandra Garkoti ◽

...

Keyword(s):

Bacterial Community ◽

Bacterial Diversity ◽

Community Composition ◽

Bacterial Communities ◽

Secondary Succession ◽

Positive Association ◽

Ecological Networks ◽

Growth Stages ◽

Ecosystem Recovery ◽

Soil Bacterial

Abstract This study investigated the potential role of a nitrogen-fixing early-coloniser Alnus Nepalensis D. Don (alder) in driving the changes in soil bacterial communities during secondary succession. We found that bacterial diversity was positively associated with alder growth during course of ecosystem development. Alder development elicited multiple changes in bacterial community composition and ecological networks. For example, the initial dominance of actinobacteria within bacterial community transitioned to the dominance of proteobacteria with stand development. Ecological networks approximating species associations tend to stabilize with alder growth. Janthinobacterium lividum, Candidatus Xiphinematobacter and Rhodoplanes were indicator species of different growth stages of alder. While the growth stages of alder has a major independent contribution to the bacterial diversity, its influence on the community composition was explained conjointly by the changes in soil properties with alder. Alder growth increased trace mineral element concentrations in the soil and explained 63% of variance in the Shannon-diversity. We also found positive association of alder with late-successional Quercus leucotrichophora (Oak). Together, the changes in soil bacterial community shaped by early-coloniser alder and its positive association with late-successional oak suggests a crucial role played by alder in ecosystem recovery of degraded habitats.

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Dynamics of the bacterial community in a channel catfish nursery pond with a cage–pond integration system

Canadian Journal of Microbiology ◽

10.1139/cjm-2018-0268 ◽

2018 ◽

Vol 64 (12) ◽

pp. 954-967 ◽

Cited By ~ 2

Author(s):

Liqiang Zhong ◽

Daming Li ◽

Minghua Wang ◽

Xiaohui Chen ◽

Wenji Bian ◽

...

Keyword(s):

Bacterial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Community Composition ◽

Channel Catfish ◽

Bacterial Community Composition ◽

Rrna Gene ◽

Integration System ◽

Nursery Pond ◽

Site Variation

The changes in the bacterial community composition in a channel catfish nursery pond with a cage–pond integration system were investigated by sequencing of the 16S rRNA gene through Illumina MiSeq sequencing platforms. A total of 1 362 877 sequences and 1440 operational taxonomic units were obtained. Further analysis showed that the dominant phyla in the cage and pond groups were similar, including Actinobacteria, Cyanobacteria, Proteobacteria, and Bacteroidetes, although a significant difference was detected between them by ANOSIM (P < 0.05). Temporal changes and site variation were significantly related to the variation of the bacterial community. A comprehensive analysis of the diversity and evenness of the bacterial 16S rRNA gene, redundancy analysis (RDA), and partial Mantel test showed that the bacterial community composition in a cage–pond integration system was shaped more by temporal variation than by site variation. RDA also indicated that water temperature, total dissolved solids, and Secchi depth had the largest impact on bacterial populations.

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