scholarly journals Metabolic insight into bacterial community assembly across ecosystem boundaries

2019 ◽  
Author(s):  
Nathan I. Wisnoski ◽  
Mario E. Muscarella ◽  
Megan L. Larsen ◽  
Ariane L. Peralta ◽  
Jay T. Lennon
Keyword(s):  
Community Assembly ◽  
Bacterial Communities ◽  
Regional Scale ◽  
Habitat Types ◽  
Bacterial Composition ◽  
Ecosystem Boundaries ◽  
Metabolic Heterogeneity ◽  
Persistence Strategies ◽  
Habitat Boundaries ◽  
Insight Into

ABSTRACTThe movement of organisms across habitat boundaries has important consequences for populations, communities, and ecosystems. However, because most species are not well adapted to all habitat types, dispersal into suboptimal habitats could induce physiological changes associated with persistence strategies that influence community assembly. For example, high rates of cross-boundary dispersal are thought to maintain sink populations of terrestrial bacteria in aquatic habitats, but these bacteria may also persist by lowering their metabolic activity, introducing metabolic heterogeneity that buffers the population against niche selection. To differentiate between these assembly processes, we analyzed bacterial composition along a hydrological flow path from terrestrial soils through an aquatic reservoir by sequencing the active and total (active + inactive) portions of the community. When metabolic heterogeneity was ignored, our data were consistent with views that cross-boundary dispersal is important for structuring aquatic bacterial communities. In contrast, we found evidence for strong niche selection when metabolic heterogeneity was explicitly considered, suggesting that, relative to persistence strategies, dispersal may have a weaker effect on aquatic community assembly than previously thought. By accounting for metabolic heterogeneity in complex communities, our findings clarify the roles of local- and regional-scale assembly processes in terrestrial-aquatic meta-ecosystems.

scholarly journals Metabolic insight into bacterial community assembly across ecosystem boundaries

Ecology ◽  
2020 ◽  
Vol 101 (4) ◽  
Author(s):  
Nathan I. Wisnoski ◽  
Mario E. Muscarella ◽  
Megan L. Larsen ◽  
Ariane L. Peralta ◽  
Jay T. Lennon
Keyword(s):  
Bacterial Community ◽  
Community Assembly ◽  
Ecosystem Boundaries ◽  
Insight Into

scholarly journals The capacity of wastewater treatment plants drives bacterial community structure and its assembly

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Young Kyung Kim ◽  
Keunje Yoo ◽  
Min Sung Kim ◽  
Il Han ◽  
Minjoo Lee ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Community Structure ◽  
Bacterial Community ◽  
Activated Sludge ◽  
Community Assembly ◽  
Bacterial Communities ◽  
Wastewater Treatment Plants ◽  
High Capacity ◽  
Operating Conditions ◽  
Rrna Gene

Abstract Bacterial communities in wastewater treatment plants (WWTPs) affect plant functionality through their role in the removal of pollutants from wastewater. Bacterial communities vary extensively based on plant operating conditions and influent characteristics. The capacity of WWTPs can also affect the bacterial community via variations in the organic or nutrient composition of the influent. Despite the importance considering capacity, the characteristics that control bacterial community assembly are largely unknown. In this study, we discovered that bacterial communities in WWTPs in Korea and Vietnam, which differ remarkably in capacity, exhibit unique structures and interactions that are governed mainly by the capacity of WWTPs. Bacterial communities were analysed using 16S rRNA gene sequencing and exhibited clear differences between the two regions, with these differences being most pronounced in activated sludge. We found that capacity contributed the most to bacterial interactions and community structure, whereas other factors had less impact. Co-occurrence network analysis showed that microorganisms from high-capacity WWTPs are more interrelated than those from low-capacity WWTPs, which corresponds to the tighter clustering of bacterial communities in Korea. These results will contribute to the understanding of bacterial community assembly in activated sludge processing.

scholarly journals Functional genomics study of Pseudomonas putida to determine traits associated with avoidance of a myxobacterial predator

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shukria Akbar ◽  
D. Cole Stevens
Keyword(s):  
Pseudomonas Putida ◽  
Bacterial Communities ◽  
Predator Avoidance ◽  
Phenotypic Diversity ◽  
Myxococcus Xanthus ◽  
Predator Prey ◽  
Mucoid Conversion ◽  
Small Colony ◽  
Predator Prey Models ◽  
Insight Into

AbstractPredation contributes to the structure and diversity of microbial communities. Predatory myxobacteria are ubiquitous to a variety of microbial habitats and capably consume a broad diversity of microbial prey. Predator–prey experiments utilizing myxobacteria have provided details into predatory mechanisms and features that facilitate consumption of prey. However, prey resistance to myxobacterial predation remains underexplored, and prey resistances have been observed exclusively from predator–prey experiments that included the model myxobacterium Myxococcus xanthus. Utilizing a predator–prey pairing that instead included the myxobacterium, Cystobacter ferrugineus, with Pseudomonas putida as prey, we observed surviving phenotypes capable of eluding predation. Comparative transcriptomics between P. putida unexposed to C. ferrugineus and the survivor phenotype suggested that increased expression of efflux pumps, genes associated with mucoid conversion, and various membrane features contribute to predator avoidance. Unique features observed from the survivor phenotype when compared to the parent P. putida include small colony variation, efflux-mediated antibiotic resistance, phenazine-1-carboxylic acid production, and increased mucoid conversion. These results demonstrate the utility of myxobacterial predator–prey models and provide insight into prey resistances in response to predatory stress that might contribute to the phenotypic diversity and structure of bacterial communities.

scholarly journals Modeling the temporal dynamics of cervicovaginal microbiota identifies targets that may promote reproductive health

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Alexander Munoz ◽  
Matthew R. Hayward ◽  
Seth M. Bloom ◽  
Muntsa Rocafort ◽  
Sinaye Ngcapu ◽  
...  
Keyword(s):  
High Risk ◽  
Bacterial Communities ◽  
High Probability ◽  
Temporal Dynamics ◽  
Transition Probabilities ◽  
Low Risk ◽  
Sub Saharan Africa ◽  
Reproductive Outcomes ◽  
Bacterial Composition ◽  
Sub Saharan

Abstract Background Cervicovaginal bacterial communities composed of diverse anaerobes with low Lactobacillus abundance are associated with poor reproductive outcomes such as preterm birth, infertility, cervicitis, and risk of sexually transmitted infections (STIs), including human immunodeficiency virus (HIV). Women in sub-Saharan Africa have a higher prevalence of these high-risk bacterial communities when compared to Western populations. However, the transition of cervicovaginal communities between high- and low-risk community states over time is not well described in African populations. Results We profiled the bacterial composition of 316 cervicovaginal swabs collected at 3-month intervals from 88 healthy young Black South African women with a median follow-up of 9 months per participant and developed a Markov-based model of transition dynamics that accurately predicted bacterial composition within a broader cross-sectional cohort. We found that Lactobacillus iners-dominant, but not Lactobacillus crispatus-dominant, communities have a high probability of transitioning to high-risk states. Simulating clinical interventions by manipulating the underlying transition probabilities, our model predicts that the population prevalence of low-risk microbial communities could most effectively be increased by manipulating the movement between L. iners- and L. crispatus-dominant communities. Conclusions The Markov model we present here indicates that L. iners-dominant communities have a high probability of transitioning to higher-risk states. We additionally identify transitions to target to increase the prevalence of L. crispatus-dominant communities. These findings may help guide future intervention strategies targeted at reducing bacteria-associated adverse reproductive outcomes among women living in sub-Saharan Africa.

scholarly journals New Insights on the Zeugodacus cucurbitae (Coquillett) Bacteriome

2021 ◽  
Vol 9 (3) ◽  
pp. 659
Author(s):  
Elias Asimakis ◽  
Panagiota Stathopoulou ◽  
Apostolis Sapounas ◽  
Kanjana Khaeso ◽  
Costas Batargias ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Mutual Exclusion ◽  
Bacterial Composition ◽  
Operational Taxonomic Units ◽  
Host Diet ◽  
Dominant Bacteria ◽  
High Degree

Various factors, including the insect host, diet, and surrounding ecosystem can shape the structure of the bacterial communities of insects. We have employed next generation, high-throughput sequencing of the 16S rRNA to characterize the bacteriome of wild Zeugodacus (Bactrocera) cucurbitae (Coquillett) flies from three regions of Bangladesh. The tested populations developed distinct bacterial communities with differences in bacterial composition, suggesting that geography has an impact on the fly bacteriome. The dominant bacteria belonged to the families Enterobacteriaceae, Dysgomonadaceae and Orbaceae, with the genera Dysgonomonas, Orbus and Citrobacter showing the highest relative abundance across populations. Network analysis indicated variable interactions between operational taxonomic units (OTUs), with cases of mutual exclusion and copresence. Certain bacterial genera with high relative abundance were also characterized by a high degree of interactions. Interestingly, genera with a low relative abundance like Shimwellia, Gilliamella, and Chishuiella were among those that showed abundant interactions, suggesting that they are also important components of the bacterial community. Such knowledge could help us identify ideal wild populations for domestication in the context of the sterile insect technique or similar biotechnological methods. Further characterization of this bacterial diversity with transcriptomic and metabolic approaches, could also reveal their specific role in Z. cucurbitae physiology.

scholarly journals Environment drives high phylogenetic turnover among oceanic bacterial communities

2012 ◽  
Vol 8 (4) ◽  
pp. 562-566 ◽  
Author(s):  
Thomas Pommier ◽  
Emmanuel J. P. Douzery ◽  
David Mouillot
Keyword(s):  
Bacterial Communities ◽  
Environmental Gradient ◽  
Regional Scale ◽  
Environmental Filtering ◽  
Species Level ◽  
Geographical Distance ◽  
Abiotic Conditions ◽  
High Connectivity ◽  
Phylogenetic Lineages ◽  
Marine Microbial Communities

Although environmental filtering has been observed to influence the biodiversity patterns of marine bacterial communities, it was restricted to the regional scale and to the species level, leaving the main drivers unknown at large biogeographic scales and higher taxonomic levels. Bacterial communities with different species compositions may nevertheless share phylogenetic lineages, and phylogenetic turnover (PT) among those communities may be surprisingly low along any biogeographic or environmental gradient. Here, we investigated the relative influence of environmental filtering and geographical distance on the PT between marine bacterial communities living more than 8000 km apart in contrasted abiotic conditions. PT was high between communities and was more structured by local environmental factors than by geographical distance, suggesting the predominance of a lineage filtering process. Strong phenotype-environment mismatches observed in the ocean may surpass high connectivity between marine microbial communities.

scholarly journals Rhizosphere Bacteria Exhibit Narrower Environmental Adaptation in Proso Millet Than in Foxtail Millet and Sorghum in Agricultural Fields

2021 ◽  
Author(s):  
Lixin Tian ◽  
Feifei Zhang ◽  
Pengliang Chen ◽  
Panpan Zhang ◽  
Zhijun Gao ◽  
...  
Keyword(s):  
Community Assembly ◽  
Bacterial Communities ◽  
Large Scale ◽  
Foxtail Millet ◽  
Environmental Adaptation ◽  
Rhizosphere Bacteria ◽  
Agricultural Fields ◽  
Proso Millet ◽  
Rhizosphere Community ◽  
Rhizosphere Bacterial Communities

Abstract It is of great ecological significance to understand how the assembly processes of soil microbe communities respond to environmental change. However, the assembly processes of the rhizosphere bacterial communities in three minor grain crops (i.e., foxtail millet, proso millet, and sorghum) across agro-ecosystems are rarely investigated. Here, we investigated the environmental thresholds and phylogenetic signals for ecological preferences of rhizosphere bacterial communities of three minor grain crop taxa across complex environmental gradients to reflect their environmental adaptation. Additionally, we reported environmental factors affecting their community assembly processes based on a large-scale soil survey in agricultural fields across northern China using high-throughput sequencing.. The results demonstrated a narrower range of environmental thresholds and weaker phylogenetic signals for the ecological traits of rhizosphere bacteria in proso millet than in foxtail millet and sorghum fields, while proso millet rhizosphere community was the most phylogenetically clustered. The null model analysis indicated that homogeneous selection belonging to deterministic processes governed the sorghum rhizosphere community, whereas dispersal limitation belonging to stochastic processes was the critical assembly process in the foxtail and proso millet. Mean annual temperature was the decisive factor for adjusting the balance between stochasticity and determinism of the foxtail millet, proso millet, and sorghum rhizosphere communities. A higher temperature resulted in stochasticity in the proso millet and sorghum communities. For the foxtail millet community, the deterministic assembly increased with an increase in temperature. These results contribute to the understanding of root-associated bacterial community assembly processes in agro-ecosystems on a large scale.

scholarly journals Dispersal across habitat boundaries: uncovering the demographic fates of populations in unsuitable habitat

2021 ◽  
Author(s):  
Megan C. Szojka ◽  
Rachel M. Germain
Keyword(s):  
Temporal Variability ◽  
Adult Life ◽  
Adult Plant ◽  
Suitable Habitat ◽  
Life Stages ◽  
Habitat Types ◽  
The Matrix ◽  
Probabilistic Process ◽  
Habitat Boundaries ◽  
Matrix Patch

AbstractPatchy landscapes are characterized by abrupt transitions among distinct habitat types, forcing species to cross habitat boundaries in order to spread. Since seed dispersal is a probabilistic process, with a kernel that decays with distance, most individuals will fail to reach new, suitable habitat. Although failed dispersers are presumed dead in population models, their demographic fates may not be so simple. If transient survival is possible within unsuitable habitat, then through time, individuals may be able to reach distant, suitable habitat, forming new populations and buffering species from extinction. In a fragmented Californian grassland, we explored the fates of individuals that crossed habitat boundaries, and if those fates differed among specialists dispersing from two habitat types: serpentine habitat patches and the invaded non-serpentine matrix. We surveyed the diversity of seedbank and adult life stages along transects that crossed boundaries between patches and the matrix. First, we considered how patch specialists might transiently survive in the matrix via seed dormancy or stepping-stone populations. Second, we investigated the dispersal of an invasive matrix specialist (Avena fatua) into patches, to assess if sink populations existed across the habitat boundary. We found that dormancy maintained populations of patch specialists deep into the matrix, as abundances of seedbanks and of adult plant communities differed with distance into the matrix. We found evidence that these dormant seeds disperse secondarily with vectors of material flows in the landscape, suggesting that they could eventually reach suitable patches even if they first land in the matrix. We found that A. fatua were largely absent deep in patches, where reproductive outputs plummeted and there was no evidence of a dormant seedbank. Our results not only reveal the demographic fates of individuals that land in unsuitable habitat, but that their ecological consequences differ depending on the direction by which the boundary is crossed (patch → matrix ≠ matrix → patch). Dormancy is often understood as a mechanism for persisting in face of temporal variability, but it may serve as a means of traversing unsuitable habitat in patchy systems, warranting its consideration in estimates of habitat connectivity.

scholarly journals Depression of Groundwater Table and Reduced Nitrogen Application Jointly Regulate the Bacterial Composition of nirS-Type and nirK-Type Genes in Agricultural Soil

Water ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 3459
Author(s):  
Fangfang Bai ◽  
Xuebin Qi ◽  
Ping Li ◽  
Dongmei Qiao ◽  
Jianming Wang ◽  
...  
Keyword(s):  
Species Composition ◽  
Nitrogen Fertilization ◽  
Bacterial Communities ◽  
Agricultural Soil ◽  
Soil Microbial Communities ◽  
Groundwater Table ◽  
Nitrogen Application ◽  
Bacterial Composition ◽  
Reduced Nitrogen ◽  
The Impact

Despite the known influence of nitrogen fertilization and groundwater conditions on soil microbial communities, the effects of their interactions on bacterial composition of denitrifier communities have been rarely quantified. Therefore, a large lysimeter experiment was conducted to examine how and to what extent groundwater table changes and reduced nitrogen application would influence the bacterial composition of nirK-type and nirS-type genes. The bacterial composition of nirK-type and nirS-type genes were compared at two levels of N input and three groundwater table levels. Our results demonstrated that depression of groundwater table, reduced nitrogen application and their interactions would lead to drastic shifts in the bacterial composition of nirS-type and nirK-type genes. Structural equation models (SEMs) indicated that depression of groundwater table and reduced nitrogen application not only directly altered the species composition of denitrifier bacterial communities, but also indirectly influenced them through regulating soil nutrient and salinity. Furthermore, the variation in soil NO3−–N and electrical conductivity caused by depression of groundwater table and reduced nitrogen application played the most important role in altering the community composition of denitrifier bacterial communities. Together, our findings provide first-hand evidence that depression of groundwater table and reduced nitrogen application jointly regulate the species composition of denitrifier bacterial communities in agricultural soil. We highlight that local environmental conditions such as groundwater table and soil attributes should be taken into account to enrich our knowledge of the impact of nitrogen fertilization on soil denitrifier bacterial communities, or even biogeochemical cycles.

Sign in / Sign up

Export Citation Format

Share Document