Host Species and Geography Differentiate Honeybee Gut Bacterial Communities by Changing the Relative Contribution of Community Assembly Processes

Honeybees provide crucial pollination services and valuable apiarian products. The symbiotic intestinal communities facilitate honeybee health and fitness by promoting nutrient assimilation, detoxifying toxins, and resisting pathogens.

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Evaluating host to host transplants as a method to study plant bacterial assembly

10.1101/2021.08.30.458296 ◽

2021 ◽

Author(s):

Christopher M Baldock ◽

Neil Wilson ◽

Rosalind Deaker

Keyword(s):

Community Assembly ◽

Host Species ◽

Bacterial Communities ◽

Host Plants ◽

Major Step ◽

Ecological Processes ◽

Surrogate Host ◽

New Hosts ◽

Species Specific ◽

Microbiome Assembly

The ability to predict plant microbiome assembly will enable new bacterial-based technologies for agriculture. A major step towards this is quantifying the roles of ecological processes on community assembly. This is challenging, in part because individuals within a populations of host plants may be colonised by different assemblages of bacteria, simply because of variation in soil communities proximal to said plants. This creates uncertainty because it is difficult to estimate if the absence of a given species was a) because it was not present to colonise the plant or b) it went locally extinct from competition, predation or similar. To address this, the authors develop a mesocosm system to study bacterial communities of individual plants by replicated transplantation to a recipient host plant population, ensuring new hosts receive a homogenous species pool for colonisation. We sought to understand which factors affected the transplant and, what the main drivers of variation in the model communities were. A nested factorial design was used to investigate the transplantation of cultured or total, root or leaf associated bacterial communities from donor host species to surrogate host species. Specific metrics were developed to quantify colonisation efficiency of communities. The results show the root communities were more effectively transplanted than leaf communities, and a higher proportion of cultured communities were recovered than total communities. For root communities the strongest drivers of beta diversity was the donor host species, and for leaves it was the surrogate host species. Overall the results reveal that root, but not leaf communities are suited to this system reflecting their differing ecological drivers.

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

Scientific Reports ◽

10.1038/s41598-019-50952-0 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 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.

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The dilution effect limits plasmid horizontal transmission in multispecies bacterial communities

Microbiology ◽

10.1099/mic.0.001086 ◽

2021 ◽

Vol 167 (9) ◽

Author(s):

Anastasia Kottara ◽

Laura Carrilero ◽

Ellie Harrison ◽

James P. J. Hall ◽

Michael A. Brockhurst

Keyword(s):

Host Species ◽

Bacterial Communities ◽

Horizontal Transmission ◽

Dilution Effect ◽

Infection Risk ◽

Host Cells ◽

Evolutionary Innovation ◽

Genomic Divergence ◽

Plasmid Diversity ◽

Plasmid Conjugation

By transferring ecologically important traits between species, plasmids drive genomic divergence and evolutionary innovation in their bacterial hosts. Bacterial communities are often diverse and contain multiple coexisting plasmids, but the dynamics of plasmids in multi-species communities are poorly understood. Here, we show, using experimental multi-species communities containing two plasmids, that bacterial diversity limits the horizontal transmission of plasmids due to the ‘dilution effect’; this is an epidemiological phenomenon whereby living alongside less proficient host species reduces the expected infection risk for a focal host species. In addition, plasmid horizontal transmission was also affected by plasmid diversity, such that the rate of plasmid conjugation was reduced from co-infected host cells carrying both plasmids. In diverse microbial communities, plasmid spread may be limited by the dilution effect and plasmid–plasmid interactions, reducing the rate of horizontal transmission.

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

10.21203/rs.3.rs-938046/v1 ◽

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.

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Host species, pathogens and disease associated with divergent nasal microbial communities in tortoises

Royal Society Open Science ◽

10.1098/rsos.181068 ◽

2018 ◽

Vol 5 (10) ◽

pp. 181068

Author(s):

Chava L. Weitzman ◽

Franziska C. Sandmeier ◽

C. Richard Tracy

Keyword(s):

Host Species ◽

Bacterial Communities ◽

Sonoran Desert ◽

Bacterial Community Composition ◽

Operational Taxonomic Unit ◽

Nasal Discharge ◽

Microbiome Composition ◽

Technological Advances ◽

Repeated Sampling ◽

Pathogen Colonization

Diverse bacterial communities are found on every surface of macro-organisms, and they play important roles in maintaining normal physiological functions in their hosts. While the study of microbiomes has expanded with the influx of data enabled by recent technological advances, microbiome research in reptiles lags behind other organisms. We sequenced the nasal microbiomes in a sample of four North American tortoise species, and we found differing community compositions among tortoise species and sampling sites, with higher richness and diversity in Texas and Sonoran desert tortoises. Using these data, we investigated the prevalence and operational taxonomic unit (OTU) diversity of the potential pathogen Pasteurella testudinis and found it to be common, abundant and highly diverse. However, the presence of this bacterium was not associated with differences in bacterial community composition within host species. We also found that the presence of nasal discharge from tortoises at the time of sampling was associated with a decline in diversity and a change in microbiome composition, which we posit is due to the harsh epithelial environment associated with immune responses. Repeated sampling across seasons, and at different points of pathogen colonization, should contribute to our understanding of the causes and consequences of different bacterial communities in these long-lived hosts.

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Bacterial community assembly in Atlantic cod larvae (Gadus morhua): contributions of ecological processes and metacommunity structure

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa163 ◽

2020 ◽

Vol 96 (9) ◽

Cited By ~ 1

Author(s):

Ragnhild I Vestrum ◽

Kari J K Attramadal ◽

Olav Vadstein ◽

Madeleine Stenshorne Gundersen ◽

Ingrid Bakke

Keyword(s):

Community Assembly ◽

Bacterial Communities ◽

Atlantic Cod ◽

Animal Health ◽

Striking Difference ◽

Ecological Processes ◽

Opportunistic Bacteria ◽

Atlantic Cod Larvae ◽

Microbe Interactions ◽

Host Microbe Interactions

ABSTRACT Many studies demonstrate the importance of the commensal microbiomes to animal health and development. However, the initial community assembly process is poorly understood. It is unclear to what extent the hosts select for their commensal microbiota, whether stochastic processes contribute, and how environmental conditions affect the community assembly. We investigated community assembly in Atlantic cod larvae exposed to distinct microbial metacommunities. We aimed to quantify ecological processes influencing community assembly in cod larvae and to elucidate the complex relationship between the bacteria of the environment and the fish. Selection within the fish was the major determinant for community assembly, but drift resulted in inter-individual variation. The environmental bacterial communities were highly dissimilar from those associated with the fish. Still, differences in the environmental bacterial communities strongly influenced the fish communities. The most striking difference was an excessive dominance of a single OTU (Arcobacter) for larvae reared in two of the three systems. These larvae were exposed to environments with higher fractions of opportunistic bacteria, and we hypothesise that detrimental host–microbe interactions might have made the fish susceptible to Arcobacter colonisation. Despite strong selection within the host, this points to a possibility to steer the metacommunity towards mutualistic host–microbe interactions and improved fish health and survival.

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Pollination by hoverflies in the Anthropocene

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2020.0508 ◽

2020 ◽

Vol 287 (1927) ◽

pp. 20200508 ◽

Cited By ~ 7

Author(s):

Toby Doyle ◽

Will L. S. Hawkes ◽

Richard Massy ◽

Gary D. Powney ◽

Myles H. M. Menz ◽

...

Keyword(s):

Crop Protection ◽

Ecosystem Functions ◽

Anthropogenic Change ◽

Migratory Species ◽

Long Distance ◽

Pollination Services ◽

Relative Contribution ◽

Or Groups ◽

Large Populations ◽

Global Food

Pollinator declines, changes in land use and climate-induced shifts in phenology have the potential to seriously affect ecosystem function and food security by disrupting pollination services provided by insects. Much of the current research focuses on bees, or groups other insects together as ‘non-bee pollinators’, obscuring the relative contribution of this diverse group of organisms. Prominent among the ‘non-bee pollinators’ are the hoverflies, known to visit at least 72% of global food crops, which we estimate to be worth around US$300 billion per year, together with over 70% of animal pollinated wildflowers. In addition, hoverflies provide ecosystem functions not seen in bees, such as crop protection from pests, recycling of organic matter and long-distance pollen transfer. Migratory species, in particular, can be hugely abundant and unlike many insect pollinators, do not yet appear to be in serious decline. In this review, we contrast the roles of hoverflies and bees as pollinators, discuss the need for research and monitoring of different pollinator responses to anthropogenic change and examine emerging research into large populations of migratory hoverflies, the threats they face and how they might be used to improve sustainable agriculture.

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Evolutionary History Impacts Phyllosphere Community Assembly on Forage Grasses

10.1101/2021.06.15.448595 ◽

2021 ◽

Author(s):

Emily K. Bechtold ◽

Klaus Nüsslein

Keyword(s):

Drought Stress ◽

Microbial Communities ◽

Community Assembly ◽

Host Species ◽

Evolutionary History ◽

Plant Traits ◽

Evolutionary Relationship ◽

Grass Species ◽

Plant Hosts ◽

Over Time

Benefits leaf bacterial communities provide to plant hosts are reduced by external stress. Understanding how plant hosts impact phyllosphere community assembly, how microbes influence plant traits, and how this interaction changes under stress will advance our insight into the evolutionary relationship between plants and their microbial communities. We investigated phyllosphere community assembly change over time, between host species, and under drought stress on three native temperate grasses and three non-native tropical grasses. By growing them together, effects of host geography and differences in environmental variables were eliminated allowing us to test evolutionary history on community assembly. We found evidence of phylosymbiosis which increased significantly under drought stress, indicating phyllosphere communities and their response to stress relate to grass species phylogeny. We also show native temperate grasses displayed stronger cophylogenetic relationships between grass hosts and their microbial communities and had increased selection by host species over time compared to non-native tropical hosts. Interestingly, the functional marker gene nifH, though differentially present on all host species was not susceptible to drought. The evidence of shared evolutionary history, presence of functionally important bacteria, and responses to drought suggest that microbial communities are important plant traits that coevolve alongside their plant hosts.

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Tree phyllosphere bacterial communities: exploring the magnitude of intra- and inter-individual variation among host species

PeerJ ◽

10.7717/peerj.2367 ◽

2016 ◽

Vol 4 ◽

pp. e2367 ◽

Cited By ~ 42

Author(s):

Isabelle Laforest-Lapointe ◽

Christian Messier ◽

Steven W. Kembel

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Individual Variation ◽

Host Species ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Temperate Forest ◽

Abies Balsamea ◽

Tree Canopy ◽

Individual Tree

BackgroundThe diversity and composition of the microbial community of tree leaves (the phyllosphere) varies among trees and host species and along spatial, temporal, and environmental gradients. Phyllosphere community variation within the canopy of an individual tree exists but the importance of this variation relative to among-tree and among-species variation is poorly understood. Sampling techniques employed for phyllosphere studies include picking leaves from one canopy location to mixing randomly selected leaves from throughout the canopy. In this context, our goal was to characterize the relative importance of intra-individual variation in phyllosphere communities across multiple species, and compare this variation to inter-individual and interspecific variation of phyllosphere epiphytic bacterial communities in a natural temperate forest in Quebec, Canada.MethodsWe targeted five dominant temperate forest tree species including angiosperms and gymnosperms:Acer saccharum,Acer rubrum,Betula papyrifera,Abies balsameaandPicea glauca. For one randomly selected tree of each species, we sampled microbial communities at six distinct canopy locations: bottom-canopy (1–2 m height), the four cardinal points of mid-canopy (2–4 m height), and the top-canopy (4–6 m height). We also collected bottom-canopy leaves from five additional trees from each species.ResultsBased on an analysis of bacterial community structure measured via Illumina sequencing of the bacterial 16S gene, we demonstrate that 65% of the intra-individual variation in leaf bacterial community structure could be attributed to the effect of inter-individual and inter-specific differences while the effect of canopy location was not significant. In comparison, host species identity explains 47% of inter-individual and inter-specific variation in leaf bacterial community structure followed by individual identity (32%) and canopy location (6%).DiscussionOur results suggest that individual samples from consistent positions within the tree canopy from multiple individuals per species can be used to accurately quantify variation in phyllosphere bacterial community structure. However, the considerable amount of intra-individual variation within a tree canopy ask for a better understanding of how changes in leaf characteristics and local abiotic conditions drive spatial variation in the phyllosphere microbiome.

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Turnover is replaced by nestedness with increasing geographical distance in bacterial communities of coastal shallow lakes

Marine and Freshwater Research ◽

10.1071/mf19110 ◽

2020 ◽

Vol 71 (9) ◽

pp. 1086

Author(s):

Marla Sonaira Lima ◽

Fabiana Schneck ◽

Ng Haig They ◽

Luciane Oliveira Crossetti ◽

Juliana Elisa Bohnenberger ◽

...

Keyword(s):

Shallow Lakes ◽

Bacterial Communities ◽

Local Environment ◽

Dispersal Limitation ◽

Geographical Distance ◽

Environmental Filters ◽

Species Sorting ◽

Relative Contribution ◽

Β Diversity ◽

The Relationship

In this study we measured the relative contribution of two components of β-diversity, turnover and nestedness, of bacterioplankton among 25 shallow lakes in southern Brazil and tested their relationship with local (environment, chlorophyll-a and biomass of phytoplanktonic classes) and landscape variables, as well as geographical distance. We predicted that turnover would be the largest share of total β-diversity due to the variation of local characteristics among lakes. Further, we expected nestedness to increase at the expense of turnover with increasing geographical distance among lakes due to dispersal limitation. The results indicated a higher contribution of turnover than nestedness to total β-diversity, which was driven by local factors. When the relationship between β-diversity components and the spatial extent between each lake and all other lakes was considered, turnover was replaced by nestedness with increasing geographical distance for 8 (the furthermost lakes) of the 25 lakes likely because of a combination of decreasing dispersal due to distance and richness differences due to wind-driven mass effects. The results of this study suggest a role for nestedness as an indicator of dispersal limitation owing to geographical distance and wind dispersal, and for turnover as an indicator of species sorting because of environmental filters for these freshwater bacterial communities.

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