Local adaptation, geographical distance and phylogenetic relatedness: assessing the drivers of siderophore‐mediated social interactions in natural bacterial communities

AbstractIn heterogenous, spatially structured habitats, individuals within populations can become adapted to the prevailing conditions in their local environment. Such local adaptation has been reported for animals and plants, and for pathogens adapting to hosts. There is increasing interest in applying the concept of local adaptation to microbial populations, especially in the context of microbe-microbe interactions. Here, we tested whether cooperation and cheating on cooperation can spur patterns of local adaptation in soil and pond communities of Pseudomonas bacteria, collected across a geographical scale of 0.5 to 50 meters. We focused on the production of pyoverdines, a group of secreted iron-scavenging siderophores that often differ among pseudomonads in their chemical structure and the receptor required for their uptake. A combination of supernatant-feeding and competition assays between isolates from four distance categories revealed tremendous variation in the extent to which pyoverdine non- and low-producers can benefit from pyoverdines secreted by producers. However, this variation was not explained by geographical distance, but primarily depended on the phylogenetic relatedness between interacting isolates. A notable exception occurred in local pond communities, where the effect of phylogenetic relatedness was eroded in supernatant assays, probably due to the horizontal transfer of receptor genes. While the latter result could be a signature of local adaptation, our results overall indicate that common ancestry and not geographical distance is the main predictor of siderophore-mediated social interactions among pseudomonads.

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Plant regeneration from seeds responds to phylogenetic relatedness and local adaptation in Mediterranean Romulea (Iridaceae) species

Ecology and Evolution ◽

10.1002/ece3.2150 ◽

2016 ◽

Vol 6 (12) ◽

pp. 4166-4178 ◽

Cited By ~ 18

Author(s):

Angelino Carta ◽

Sarah Hanson ◽

Jonas V. Müller

Keyword(s):

Plant Regeneration ◽

Local Adaptation ◽

Phylogenetic Relatedness

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Environment drives high phylogenetic turnover among oceanic bacterial communities

Biology Letters ◽

10.1098/rsbl.2011.0990 ◽

2012 ◽

Vol 8 (4) ◽

pp. 562-566 ◽

Cited By ~ 15

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.

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Social behavior in bees influences the abundance of Sodalis (Enterobacteriaceae) symbionts

10.1101/192617 ◽

2017 ◽

Cited By ~ 1

Author(s):

Benjamin E. Rubin ◽

Jon G. Sanders ◽

Kyle M. Turner ◽

Naomi E. Pierce ◽

Sarah D. Kocher

Keyword(s):

Social Interactions ◽

Bacterial Communities ◽

Bacterial Abundance ◽

De Novo ◽

Amplicon Sequencing ◽

Social Forms ◽

Phylogenetic Reconstructions ◽

16S Amplicon Sequencing ◽

Species Specific ◽

Genome Assemblies

AbstractSocial interactions can facilitate transmission of microbes between individuals, reducing variation in gut communities within social groups. Thus, the evolution of social behaviors and symbiont community composition have the potential to be tightly linked. We explored this connection by characterizing the diversity of bacteria associated with both social and solitary bee species within the behaviorally variable family Halictidae using 16S amplicon sequencing. Contrary to expectations, we found few differences in bacterial abundance or variation between social forms, and most halictid species appear to share similar gut bacterial communities. However, several strains of Sodalis, a genus described as a symbiont in a variety of insects but yet to be characterized in bees, differ in abundance between social and solitary bees. Phylogenetic reconstructions based on whole-genome alignments indicate that Sodalis has independently colonized halictids at least three times. These strains appear to be mutually exclusive within individual bees, although they are not host-species-specific and no signatures of vertical transmission were observed, suggesting that Sodalis strains compete for access to hosts. De novo genome assemblies indicate that these three lineages are subject to widespread relaxed selection and that Sodalis is undergoing genome degeneration during the colonization of these hosts.

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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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Reproductive System Symbiotic Bacteria Are Conserved between Two Distinct Populations ofEuprymna scolopesfrom Oahu, Hawaii

mSphere ◽

10.1128/msphere.00531-17 ◽

2018 ◽

Vol 3 (2) ◽

Cited By ~ 4

Author(s):

Allison H. Kerwin ◽

Spencer V. Nyholm

Keyword(s):

Local Adaptation ◽

Relative Abundance ◽

Bacterial Communities ◽

Model Organism ◽

Amplicon Sequencing ◽

Host Population ◽

Euprymna Scolopes ◽

Isolated Populations ◽

Content Type ◽

Kaneohe Bay

ABSTRACTFemale Hawaiian bobtail squid,Euprymna scolopes, harbor a symbiotic bacterial community in a reproductive organ, the accessory nidamental gland (ANG). This community is known to be stable over several generations of wild-caught bobtail squid but has, to date, been examined for only one population in Maunalua Bay, Oahu, HI. This study assessed the ANG and corresponding egg jelly coat (JC) bacterial communities for another genetically isolated host population from Kaneohe Bay, Oahu, HI, using 16S amplicon sequencing. The bacterial communities from the ANGs and JCs of the two populations were found to be similar in richness, evenness, phylogenetic diversity, and overall community composition. However, the Kaneohe Bay samples formed their own subset within the Maunalua Bay ANG/JC community. AnAlteromonadaceaegenus, BD2-13, was significantly higher in relative abundance in the Kaneohe Bay population, and severalAlphaproteobacteriataxa also shifted in relative abundance between the two groups. This variation could be due to local adaptation to differing environmental challenges, to localized variability, or to functional redundancy among the ANG taxa. The overall stability of the community between the populations further supports a crucial functional role that has been hypothesized for this symbiosis.IMPORTANCEIn this study, we examined the reproductive ANG symbiosis found in two genetically isolated populations of the Hawaiian bobtail squid,Euprymna scolopes. The stability of the community reported here provides support for the hypothesis that this symbiosis is under strong selective pressure, while the observed differences suggest that some level of local adaptation may have occurred. These two host populations are frequently used interchangeably as source populations for research.Euprymna scolopesis an important model organism and offers the opportunity to examine the interplay between a binary and a consortial symbiosis in a single model host. Understanding the inherent natural variability of this association will aid in our understanding of the conservation, function, transmission, and development of the ANG symbiosis.

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Accumulation of dead cells from contact killing facilitates coexistence in bacterial biofilms

10.1101/2020.04.03.024158 ◽

2020 ◽

Author(s):

Gabi Steinbach ◽

Cristian Crisan ◽

Siu Lung Ng ◽

Brian Hammer ◽

Peter Yunker

Keyword(s):

Social Interactions ◽

Bacterial Communities ◽

Target Cells ◽

Dead Cell ◽

Type Vi Secretion System ◽

Cell Debris ◽

Cell Level ◽

Bacterial Populations ◽

Type Vi Secretion ◽

The Impact

AbstractBacterial communities govern their composition using a wide variety of social interactions, some of which are antagonistic. Many antagonistic mechanisms, such as the Type VI Secretion System (T6SS), require killer cells to directly contact target cells. The T6SS is hypothesized to be a highly potent weapon, capable of facilitating the invasion and defense of bacterial populations. However, we find that the efficacy of the T6SS is severely limited by the material consequences of cell death. Through experiments with Vibrio cholerae strains that kill via the T6SS, we show that dead cell debris quickly accumulates at the interface that forms between competing strains, preventing contact and thus preventing killing. While previous experiments have shown that T6SS killing can reduce a population of target cells by as much as one-million-fold, we find that as a result of the formation of dead cell debris barriers, the impact of T6SS killing depends sensitively on the initial concentrations of killer and target cells. Therefore, while the T6SS provides defense against contacting competitors on a single cell level, it is incapable of facilitating invasion or the elimination of competitors on a community level.

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Social behaviour in bees influences the abundance of Sodalis (Enterobacteriaceae) symbionts

Royal Society Open Science ◽

10.1098/rsos.180369 ◽

2018 ◽

Vol 5 (7) ◽

pp. 180369 ◽

Cited By ~ 5

Author(s):

Benjamin E. R. Rubin ◽

Jon G. Sanders ◽

Kyle M. Turner ◽

Naomi E. Pierce ◽

Sarah D. Kocher

Keyword(s):

Social Interactions ◽

Bacterial Communities ◽

Bacterial Abundance ◽

Social Groups ◽

Amplicon Sequencing ◽

Solitary Bee ◽

Social Forms ◽

Phylogenetic Reconstructions ◽

16S Amplicon Sequencing ◽

Species Specific

Social interactions can facilitate transmission of microbes between individuals, reducing variation in gut communities within social groups. Thus, the evolution of social behaviours and symbiont community composition have the potential to be tightly linked. We explored this connection by characterizing the diversity of bacteria associated with both eusocial and solitary bee species within the behaviourally variable family Halictidae using 16S amplicon sequencing. Contrary to expectations, we found few differences in bacterial abundance or variation between social forms; most halictid species appear to share similar gut bacterial communities. However, several strains of Sodalis, a genus described as a symbiont in a variety of insects but yet to be characterized in bees, differ in abundance between eusocial and solitary bees. Phylogenetic reconstructions based on whole-genome alignments indicate that Sodalis has independently colonized halictids at least three times. These strains appear to be mutually exclusive within individual bees, although they are not host-species-specific and no signatures of vertical transmission were observed, suggesting that Sodalis strains compete for access to hosts. The symbiosis between halictids and Sodalis therefore appears to be in its early stages.

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Spatial patterns in phage-Rhizobium coevolutionary interactions across regions of common bean domestication

10.1101/2020.07.21.214783 ◽

2020 ◽

Author(s):

Jannick Van Cauwenberghe ◽

Rosa I. Santamaría ◽

Patricia Bustos ◽

Soledad Juárez ◽

Maria Antonella Ducci ◽

...

Keyword(s):

Common Bean ◽

Local Adaptation ◽

Bacterial Communities ◽

Geographic Origin ◽

Cross Infection ◽

Symbiotic Bacteria ◽

Infection Rates ◽

Host Interactions ◽

Host Diversity

AbstractBacteriophages play significant roles in the composition, diversity, and evolution of bacterial communities. Despite their importance, it remains unclear how phage diversity and phage-host interactions are spatially structured. Local adaptation may play a key role. Nitrogen-fixing symbiotic bacteria, known as rhizobia, have been shown to locally adapt to domesticated common bean at its Mesoamerican and Andean sites of origin. This may affect phage-rhizobium interactions. However, knowledge about the diversity and coevolution of phages with their respective Rhizobium populations is lacking. Here, through the study of four phage-Rhizobium communities in Mexico and Argentina, we show that both phage and host diversity is spatially structured. Cross-infection experiments demonstrated that phage infection rates were higher overall in sympatric rhizobia than in allopatric rhizobia except for one Argentinean community, indicating phage local adaptation and host maladaptation. Phage-host interactions were shaped by the genetic identity and geographic origin of both the phage and the host. The phages ranged from specialists to generalists, revealing a nested network of interactions. Our results suggest a key role of local adaptation to resident host bacterial communities in shaping the phage genetic and phenotypic composition, following a similar spatial pattern of diversity and coevolution to that in the host.

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