The importance of physical isolation to microbial diversification

Distinct Assembly Patterns of Soil Bacterial and Fungal Communities along Altitudinal Gradients in the Loess Plateau's Highest Mountain

A critical issue in microbial ecology is quantifying the relative contributions of deterministic and stochastic processes to microbial community assembly, and predicting ecosystem function by understanding the ecological processes of community composition is an integral part. However, the mechanisms driving microbial community assembly along altitudinal gradients in mountain ecosystems remain largely unexplored. Here, we used high-throughput sequencing to examine the structural characteristics and diversity maintenance mechanisms of soil bacterial and fungal communities along an altitudinal gradient (2632-3661 m) in Mahan Mountain, the highest peak of the Loess Plateau. Proteobacteria, Acidobacteriota and Actinobacteriota dominated the bacterial communities, while Ascomycota, Basidiomycota and Mortierellomycota were the predominant fungal groups. Although elevation did not significantly affect bacterial and fungal alpha diversity, notable shifts in community structure were observed along the altitudinal gradients. Bacterial communities were predominantly shaped by deterministic processes, leading to pronounced structural and compositional differentiation across altitudes. In contrast, fungal community assembly was primarily determined by a combination of deterministic and stochastic processes, leading to small pronounced structural divergence. The interplay of topography, climate, and soil conditions influenced the altitudinal distribution and community structure of soil bacteria in this mountain ecosystem.

Screening of oxytetracycline-degrading strains in the intestine of the black soldier fly larvae and their degradation characteristics

The presence of excessive antibiotic residues poses a significant threat to human health and the environment. This study was designed to identify an effective oxytetracycline (OTC)-degrading strain through the screening of the intestine of black soldier fly larvae (BSFL). A strain designated "B2" was selected using a series of traditional microbial screening methods. It could be identified as Enterococcus faecalis by Gram staining and 16S rDNA sequencing, with a similarity of 99.93%. Its ability to degrade OTC was then assessed using high-performance liquid chromatography (HPLC). The degradation of the strain was characterized using a one-way test to assess the effects of the substrate concentration, inoculum amount, and initial pH on the degrading bacteria. The results indicate that strain B2 exhibited optimal OTC-degrading performance at a substrate concentration of 50 mg/L, with an inoculum amount of 6% and a pH value of 5.0. Specifically, strain B2 achieved degradation rates of 71.11%, 56.14%, and 45.03%. These findings demonstrate the effectiveness of strain B2 in degrading OTC, indicating its potential for use in environmental remediation efforts.

Barley farmland harbors a highly homogeneous soil bacterial community compared to wild ecosystems in the Qinghai-Xizang Plateau

Introduction

Understanding patterns and processes of microbial biogeography in soils is important for monitoring ecological responses to human activities, particularly in ecologically vulnerable areas such as the Qinghai-Xizang Plateau. Highland barley is the staple food of local people and has mainly been cultivated along the Yarlung Zangbo River valley in Xizang.

Methods

Here we investigated soil bacterial communities from 33 sampling sites of highland barley farmland in this region and compared them to those from wild ecosystems including alpine tundra, meadow, forest, and swamp. Additionally, the effects of environmental factors on bacterial communities, as well as the relative importance of stochastic and deterministic processes in shaping the beta diversity of soil bacterial communities in alpine ecosystems were assessed.

Results

In contrast to soils of wild ecosystems, these farmland samples harbored a highly homogeneous bacterial community without significant correlations with geographic, elevation, and edaphic distances. Discriminant bacterial taxa identified for farmland samples belong to Acidobacteria, with Acidobacteria Gp4 as the dominant clade. Although Acidobacteria were the most abundant members in all ecosystems, characterized bacterial taxa of meadow and forest were members of other phyla such as Proteobacteria and Verrucomicrobia. pH and organic matter were major edaphic attributes shaping these observed patterns across ecosystems. Null model analyses revealed that the deterministic assembly was dominant in bacterial communities in highland barley farmland and tundra soils, whereas stochastic assembly also contributed a large fraction to the assembly of bacterial communities in forest, meadow and swamp soils.

Discussion

These findings provide an insight into the consequences of human activities and agricultural intensification on taxonomic homogenization of soil bacterial communities in the Qinghai-Xizang Plateau.

Distinct biogeographical patterns in snail gastrointestinal tract bacterial communities compared with sediment and water

The factors that influence the distribution of bacterial community composition are not well understood. The role of geographical patterns, which suggest limited dispersal, is still a topic of debate. Bacteria associated with hosts face unique dispersal challenges as they often rely on their hosts, which provide specific environments for their symbionts. In this study, we examined the effect of biogeographic distances on the bacterial diversity and composition of bacterial communities in the gastrointestinal tract of Ampullaceana balthica. We compared the effects on the host-associated bacterial community to those on bacterial communities in water and sediment. This comparison was made using 16S ribosomal RNA gene sequencing. We found that the bacterial communities we sampled in Estonia, Denmark, and Northern Germany varied between water, sediment, and the gastrointestinal tract. They also varied between countries within each substrate. This indicates that the type of substrate is a dominant factor in determining bacterial community composition. We separately analyzed the turnover rates of water, sediment, and gastrointestinal bacterial communities over increasing geographic distances. We observed that the turnover rate was lower for gastrointestinal bacterial communities compared to water bacterial communities. This implies that the composition of gastrointestinal bacteria remains relatively stable over distances, while water bacterial communities exhibit greater variability. However, the gastrointestinal tract had the lowest percentage of country-specific amplicon sequence variants, suggesting bacterial colonization from local bacterial communities. Since the overlap between the water and gastrointestinal tract was highest, it appears that the gastrointestinal bacterial community is colonized by the water bacterial community. Our study confirmed that biogeographical patterns in host-associated communities differ from those in water and sediment bacterial communities. These host-associated communities consist of numerous facultative symbionts derived from the water bacterial community.

The Mystery of Piezophiles: Understudied Microorganisms from the Deep, Dark Subsurface

Microorganisms that can withstand high pressure within an environment are termed piezophiles. These organisms are considered extremophiles and inhabit the deep marine or terrestrial subsurface. Because these microorganisms are not easily accessed and require expensive sampling methods and laboratory instruments, advancements in this field have been limited compared to other extremophiles. This review summarizes the current knowledge on piezophiles, notably the cellular and physiological adaptations that such microorganisms possess to withstand and grow in high-pressure environments. Based on existing studies, organisms from both the deep marine and terrestrial subsurface show similar adaptations to high pressure, including increased motility, an increase of unsaturated bonds within the cell membrane lipids, upregulation of heat shock proteins, and differential gene-regulation systems. Notably, more adaptations have been identified within the deep marine subsurface organisms due to the relative paucity of studies performed on deep terrestrial subsurface environments. Nevertheless, similar adaptations have been found within piezophiles from both systems, and therefore the microbial biogeography concepts used to assess microbial dispersal and explore if similar organisms can be found throughout deep terrestrial environments are also briefly discussed.

Distinct taxonomic and functional profiles of high Arctic and alpine permafrost-affected soil microbiomes

BACKGROUND

Global warming is affecting all cold environments, including the European Alps and Arctic regions. Here, permafrost may be considered a unique ecosystem harboring a distinct microbiome. The frequent freeze-thaw cycles occurring in permafrost-affected soils, and mainly in the seasonally active top layers, modify microbial communities and consequently ecosystem processes. Although taxonomic responses of the microbiomes in permafrost-affected soils have been widely documented, studies about how the microbial genetic potential, especially pathways involved in C and N cycling, changes between active-layer soils and permafrost soils are rare. Here, we used shotgun metagenomics to analyze the microbial and functional diversity and the metabolic potential of permafrost-affected soil collected from an alpine site (Val Lavirun, Engadin area, Switzerland) and a High Arctic site (Station Nord, Villum Research Station, Greenland). The main goal was to discover the key genes abundant in the active-layer and permafrost soils, with the purpose to highlight the potential role of the functional genes found.

RESULTS

We observed differences between the alpine and High Arctic sites in alpha- and beta-diversity, and in EggNOG, CAZy, and NCyc datasets. In the High Arctic site, the metagenome in permafrost soil had an overrepresentation (relative to that in active-layer soil) of genes involved in lipid transport by fatty acid desaturate and ABC transporters, i.e. genes that are useful in preventing microorganisms from freezing by increasing membrane fluidity, and genes involved in cell defense mechanisms. The majority of CAZy and NCyc genes were overrepresented in permafrost soils relative to active-layer soils in both localities, with genes involved in the degradation of carbon substrates and in the degradation of N compounds indicating high microbial activity in permafrost in response to climate warming.

CONCLUSIONS

Our study on the functional characteristics of permafrost microbiomes underlines the remarkably high functional gene diversity of the High Arctic and temperate mountain permafrost, including a broad range of C- and N-cycling genes, and multiple survival and energetic metabolisms. Their metabolic versatility in using organic materials from ancient soils undergoing microbial degradation determine organic matter decomposition and greenhouse gas emissions upon permafrost thawing. Attention to their functional genes is therefore essential to predict potential soil-climate feedbacks to the future warmer climate.

Differential distribution patterns and assembly processes of soil microbial communities under contrasting vegetation types at distinctive altitudes in the Changbai Mountain

Diversity patterns and community assembly of soil microorganisms are essential for understanding soil biodiversity and ecosystem processes. Investigating the impacts of environmental factors on microbial community assembly is crucial for comprehending the functions of microbial biodiversity and ecosystem processes. However, these issues remain insufficiently investigated in related studies despite their fundamental significance. The present study aimed to assess the diversity and assembly of soil bacterial and fungal communities to altitude and soil depth variations in mountain ecosystems by using 16S and ITS rRNA gene sequence analyses. In addition, the major roles of environmental factors in determining soil microbial communities and assembly processes were further investigated. The results showed a U-shaped pattern of the soil bacterial diversity at 0-10  cm soil depth along altitudes, reaching a minimum value at 1800 m, while the fungal diversity exhibited a monotonically decreasing trend with increasing altitude. At 10-20  cm soil depth, the soil bacterial diversity showed no apparent changes along altitudinal gradients, while the fungal Chao1 and phylogenetic diversity (PD) indices exhibited hump-shaped patterns with increasing altitude, reaching a maximum value at 1200 m. Soil bacterial and fungal communities were distinctively distributed with altitude at the same depth of soil, and the spatial turnover rates in fungi was greater than in bacteria. Mantel tests suggested soil physiochemical and climate variables significantly correlated with the β diversity of microbial community at two soil depths, suggesting both soil and climate heterogeneity contributed to the variation of bacterial and fungal community. Correspondingly, a novel phylogenetic null model analysis demonstrated that the community assembly of soil bacterial and fungal communities were dominated by deterministic and stochastic processes, respectively. The assembly processes of bacterial community were significantly related to the soil DOC and C:N ratio, while the fungal community assembly processes were significantly related to the soil C:N ratio. Our results provide a new perspective to assess the responses of soil microbial communities to variations with altitude and soil depth.

Metabolomics Reveals a 26-Membered Macrolactone Produced by Endophytic Colletotrichum spp. from Alcatrazes Island, Brazil

Comparative metabolomics analysis of nonphytotoxic endophytic Colletotrichum spp. isolated from Anthurium alcatrazense endemic to Alcatrazes island (Brazil) and phytopathogenic Colletotrichum spp. isolated from the mainland of Brazil revealed significant differences in chemical composition. Examination of endophytic Colletotrichum spp. from Alcatrazes island led to the discovery of a 26-member macrolactone, colletotrichumolide (1), containing a phosphatidyl choline side chain. Further examination of the phytopathogenic strains from the mainland identified a family of phytopathogenic metabolites not present in the nonpathogenic island-derived strains, suggesting that geographical isolation could influence the secondary metabolism of fungal strains.

Detection and characterization of bioaerosol emissions from wastewater treatment plants: Challenges and opportunities

Rapid population growth and urbanization process have led to increasing demand for wastewater treatment capacity resulting in a non-negligible increase of wastewater treatment plants (WWTPs) in several cities around the world. Bioaerosol emissions from WWTPs may pose adverse health risks to the sewage workers and nearby residents, which raises increasing public health concerns. However, there are still significant knowledge gaps on the interplay between process-based bioaerosol characteristics and exposures and the quantification of health risk which limit our ability to design effective risk assessment and management strategies. This review provides a critical overview of the existing knowledge of bioaerosol emissions from WWTPs including their nature, magnitude and size distribution, and highlights the shortcoming associated with existing sampling and analysis methods. The recent advancements made for rapid detection of bioaerosols are then discussed, especially the emerging real time detection methods to highlight the directions for future research needs to advance the knowledge on bioaerosol emissions from WWTPs.

Redefining the Subsurface Biosphere: Characterization of Fungi Isolated From Energy-Limited Marine Deep Subsurface Sediment

The characterization of metabolically active fungal isolates within the deep marine subsurface will alter current ecosystem models and living biomass estimates that are limited to bacterial and archaeal populations. Although marine fungi have been studied for over fifty years, a detailed description of fungal populations within the deep subsurface is lacking. Fungi possess metabolic pathways capable of utilizing previously considered non-bioavailable energy reserves. Therefore, metabolically active fungi would occupy a unique niche within subsurface ecosystems, with the potential to provide an organic carbon source for heterotrophic prokaryotic populations from the transformation of non-bioavailable energy into substrates, as well as from the fungal necromass itself. These organic carbon sources are not currently being considered in subsurface energy budgets. Sediments from South Pacific Gyre subsurface, one of the most energy-limited environments on Earth, were collected during the Integrated Ocean Drilling Program Expedition 329. Anoxic and oxic sediment slurry enrichments using fresh sediment were used to isolate multiple fungal strains in media types that varied in organic carbon substrates and concentration. Metabolically active and dormant fungal populations were also determined from nucleic acids extracted from in situ cryopreserved South Pacific Gyre sediments. For further characterization of physical growth parameters, two isolates were chosen based on their representation of the whole South Pacific Gyre fungal community. Results from this study show that fungi have adapted to be metabolically active and key community members in South Pacific Gyre sediments and potentially within global biogeochemical cycles.

Shining light on a deep-sea bacterial symbiont population structure with CRISPR

Many foundation species in chemosynthesis-based ecosystems rely on environmentally acquired symbiotic bacteria for their survival. Hence, understanding the biogeographic distributions of these symbionts at regional scales is key to understanding patterns of connectivity and predicting resilience of their host populations (and thus whole communities). However, such assessments are challenging because they necessitate measuring bacterial genetic diversity at fine resolutions. For this purpose, the recently discovered clustered regularly interspaced short palindromic repeats (CRISPR) constitutes a promising new genetic marker. These DNA sequences harboured by about half of bacteria hold their viral immune memory, and as such, might allow discrimination of different lineages or strains of otherwise indistinguishable bacteria. In this study, we assessed the potential of CRISPR as a hypervariable phylogenetic marker in the context of a population genetic study of an uncultured bacterial species. We used high-throughput CRISPR-based typing along with multi-locus sequence analysis (MLSA) to characterize the regional population structure of the obligate but environmentally acquired symbiont species Candidatus Endoriftia persephone on the Juan de Fuca Ridge. Mixed symbiont populations of Ca. Endoriftia persephone were sampled across individual Ridgeia piscesae hosts from contrasting habitats in order to determine if environmental conditions rather than barriers to connectivity are more important drivers of symbiont diversity. We showed that CRISPR revealed a much higher symbiont genetic diversity than the other housekeeping genes. Several lines of evidence imply this diversity is indicative of environmental strains. Finally, we found with both CRISPR and gene markers that local symbiont populations are strongly differentiated across sites known to be isolated by deep-sea circulation patterns. This research showed the high power of CRISPR to resolve the genetic structure of uncultured bacterial populations and represents a step towards making keystone microbial species an integral part of conservation policies for upcoming mining operations on the seafloor.

Are recently deglaciated areas at both poles colonised by the same bacteria?

Polar glacier forefields offer an unprecedented framework for studying community assembly processes in regions that are geographically and climatically isolated. Through amplicon sequence variant (ASV) inference, we compared the composition and structure of soil bacterial communities from glacier forefields in Iceland and Antarctica to assess overlap between communities and the impact of established cryptogamic covers on the uniqueness of their taxa. These pioneer microbial communities were found to share only 8% of ASVs and each taxonomic group's contribution to the shared ASV data subset was heterogeneous and independent of their relative abundance. Although the presence of ASVs specific to one glacier forefield and/or different cryptogam cover values confirms the existence of habitat specialist bacteria, our data show that the influence of cryptogams on the edaphic bacterial community structure also varied also depending on the taxonomic group. Hence, the establishment of distinct cryptogamic covers is probably not the only factor driving the uniqueness of bacterial communities at both poles. The structure of bacterial communities colonising deglaciated areas seems also conditioned by lineage-specific limitations in their dispersal capacity and/or their establishment and persistence in these isolated and hostile regions.

Effects of Different Hosts on Bacterial Communities of Parasitic Wasp Nasonia vitripennis

Parasitism is a special interspecific relationship in insects. Unlike most other ectoparasites, Nasonia vitripennis spend most of its life cycle (egg, larvae, pupae, and early adult stage) inside the pupae of flies, which is covered with hard puparium. Microbes play important roles in host development and help insect hosts to adapt to various environments. How the microbes of parasitic wasp respond to different fly hosts living in such close relationships motivated this investigation. In this study, we used N. vitripennis and three different fly pupa hosts (Lucilia sericata, Sarcophaga marshalli, and Musca domestica) to address this question, as well as to illustrate the potential transfer of bacteria through the trophic food chains. We found that N. vitripennis from different fly pupa hosts showed distinct microbiota, which means that the different fly hosts could affect the bacterial communities of their parasitic wasps. Some bacteria showed potential horizontal transfer through the trophic food chains, from the food through the fly to the parasitic wasp. We also found that the heritable endosymbiont Wolbachia could transferred from the fly host to the parasite and correlated with the bacterial communities of the corresponding parasitic wasps. Our findings provide new insight to the microbial interactions between parasite and host.

Comparative Analysis of Microbial Diversity Across Temperature Gradients in Hot Springs From Yellowstone and Iceland

Geothermal hot springs are a natural setting to study microbial adaptation to a wide range of temperatures reaching up to boiling. Temperature gradients lead to distinct microbial communities that inhabit their optimum niches. We sampled three alkaline, high temperature (80-100°C) hot springs in Yellowstone and Iceland that had cooling outflows and whose microbial communities had not been studied previously. The microbial composition in sediments and mats was determined by DNA sequencing of rRNA gene amplicons. Over three dozen phyla of Archaea and Bacteria were identified, representing over 1700 distinct organisms. We observed a significant non-linear reduction in the number of microbial taxa as the temperature increased from warm (38°C) to boiling. At high taxonomic levels, the community structure was similar between the Yellowstone and Iceland hot springs. We identified potential endemism at the genus level, especially in thermophilic phototrophs, which may have been potentially driven by distinct environmental conditions and dispersal limitations.

Phylogeny, Divergent Evolution, and Speciation of Sulfur-Oxidizing Acidithiobacillus Populations

Background

Habitats colonized by acidophiles as an ideal physical barrier may induce genetic exchange of microbial members within the common communities, but little is known about how species in extremely acidic environments diverge and evolve.

Results

Using the acidophilic sulfur-oxidizer Acidithiobacillus as a case study, taxonomic reclassifications of many isolates provides novel insights into their phylogenetic lineage. Whole-genome-based comparisons were attempted to investigate the intra- and inter-species divergence. Recent studies clarified that functional and structural specificities of bacterial strains might provide opportunities for adaptive evolution responding to local environmental conditions. Acidophilic microorganisms play a key role in the acidification of natural waters and thus the formation of extremely acidic environments, and the feedbacks of the latter might confer the distinct evolutionary patterns of Acidithiobacillus spp. Varied horizontal gene transfer events occurred in different bacterial strains, probably resulting in the expansion of Acidithiobacillus genomes. Gene loss as another evolutionary force might cause the adaptive phenotypic diversity. A conceptual model for potential community-dependent evolutionary adaptation was thus proposed to illustrate the observed genome differentiation.

Conclusions

Collectively, the findings shed light on the phylogeny and divergent evolution of Acidithiobacillus strains, and provided a useful reference for evolutionary studies of other extremophiles.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5827-6) contains supplementary material, which is available to authorized users.

Living in Cold Blood: Arcobacter, Campylobacter, and Helicobacter in Reptiles

Species of the Epsilonproteobacteria genera Arcobacter, Campylobacter, and Helicobacter are commonly associated with vertebrate hosts and some are considered significant pathogens. Vertebrate-associated Epsilonproteobacteria are often considered to be largely confined to endothermic mammals and birds. Recent studies have shown that ectothermic reptiles display a distinct and largely unique Epsilonproteobacteria community, including taxa which can cause disease in humans. Several Arcobacter taxa are widespread amongst reptiles and often show a broad host range. Reptiles carry a large diversity of unique and novel Helicobacter taxa, which apparently evolved in an ectothermic host. Some species, such as Campylobacter fetus, display a distinct intraspecies host dichotomy, with genetically divergent lineages occurring either in mammals or reptiles. These taxa can provide valuable insights in host adaptation and co-evolution between symbiont and host. Here, we present an overview of the biodiversity, ecology, epidemiology, and evolution of reptile-associated Epsilonproteobacteria from a broader vertebrate host perspective.

The Biogeography of Great Salt Lake Halophilic Archaea: Testing the Hypothesis of Avian Mechanical Carriers

Halophilic archaea inhabit hypersaline ecosystems globally, and genetically similar strains have been found in locales that are geographically isolated from one another. We sought to test the hypothesis that small salt crystals harboring halophilic archaea could be carried on bird feathers and that bird migration is a driving force of these distributions. In this study, we discovered that the American White Pelicans (AWPE) at Great Salt Lake soak in the hypersaline brine and accumulate salt crystals (halite) on their feathers. We cultured halophilic archaea from AWPE feathers and halite crystals. The microorganisms isolated from the lakeshore crystals were restricted to two genera: Halorubrum and Haloarcula, however, archaea from the feathers were strictly Haloarcula. We compared partial DNA sequence of the 16S rRNA gene from our cultivars with that of similar strains in the GenBank database. To understand the biogeography of genetically similar halophilic archaea, we studied the geographical locations of the sampling sites of the closest-matched species. An analysis of the environmental factors of each site pointed to salinity as the most important factor for selection. The geography of the sites was consistent with the location of the sub-tropical jet stream where birds typically migrate, supporting the avian dispersal hypothesis.

Foliar fungal endophyte communities are structured by environment but not host ecotype in Panicum virgatum (switchgrass)

Experimental tests of community assembly mechanisms for host-associated microbiomes in nature are lacking. Asymptomatic foliar fungal endophytes are a major component of the plant microbiome and are increasingly recognized for their impacts on plant performance, including pathogen defense, hormonal manipulation, and drought tolerance. However, it remains unclear whether fungal endophytes preferentially colonize certain host ecotypes or genotypes, reflecting some degree of biotic adaptation in the symbioses, or whether colonization is simply a function of spore type and abundance within the local environment. Whether host ecotype, local environment, or some combination of both controls the pattern of microbiome formation across hosts represents a new dimension to the age-old debate of nature versus nurture. Here, we used a reciprocal transplant design to explore the extent of host specificity and biotic adaptation in the plant microbiome, as evidenced by differential colonization of host genetic types by endophytes. Specifically, replicate plants from three locally-adapted ecotypes of the native grass Panicum virgatum (switchgrass) were transplanted at three geographically distinct field sites (one home and two away) in the Midwestern US. At the end of the growing season, plant leaves were harvested and the fungal microbiome characterized using culture-dependent sequencing techniques. Our results demonstrated that fungal endophyte community structure was determined by local environment (i.e., site), but not by host ecotype. Fungal richness and diversity also strongly differed by site, with lower fungal diversity at a riparian field site, whereas host ecotype had no effect. By contrast, there were significant differences in plant phenotypes across all ecotypes and sites, indicating ecotypic differentiation of host phenotype. Overall, our results indicate that environmental factors are the primary drivers of community structure in the switchgrass fungal microbiome.

DYNAMICS OF AN INSERTION SEQUENCE INFECTION IN A SPATIALLY STRUCTURED ENVIRONMENT

Bacterial insertion sequences (ISs), the simplest form of autonomous mobile DNA, depend on their prokaryote hosts to spread in a spatially structured environment. We use a spatially explicit metapopulation model to simulate the spread of an IS that can have both detrimental and beneficial effects on its host cell. We find that, on the one hand, the spatial structure of the metapopulation and cell dispersal between subpopulations have no strong effect on the time to full infection of the metapopulation. On the other hand, factors that influence the IS infection dynamics within a subpopulation have a strong effect on that time. These factors are mainly the fitness benefit of an IS and the rate of horizontal gene transfer. We also find that the infection process of a metapopulation is very erratic in its early phase. Finally, we show that the infection’s success depends critically on the initially infected subpopulation.

The Coevolution of Life and Environment on Mars: An Ecosystem Perspective on the Robotic Exploration of Biosignatures

Earth's biological and environmental evolution are intertwined and inseparable. This coevolution has become a fundamental concept in astrobiology and is key to the search for life beyond our planet. In the case of Mars, whether a coevolution took place is unknown, but analyzing the factors at play shows the uniqueness of each planetary experiment regardless of similarities. Early Earth and early Mars shared traits. However, biological processes on Mars, if any, would have had to proceed within the distinctive context of an irreversible atmospheric collapse, greater climate variability, and specific planetary characteristics. In that, Mars is an important test bed for comparing the effects of a unique set of spatiotemporal changes on an Earth-like, yet different, planet. Many questions remain unanswered about Mars' early environment. Nevertheless, existing data sets provide a foundation for an intellectual framework where notional coevolution models can be explored. In this framework, the focus is shifted from planetary-scale habitability to the prospect of habitats, microbial ecotones, pathways to biological dispersal, biomass repositories, and their meaning for exploration. Critically, as we search for biosignatures, this focus demonstrates the importance of starting to think of early Mars as a biosphere and vigorously integrating an ecosystem approach to landing site selection and exploration. Key Words: Astrobiology-Biosignatures-Coevolution of Earth and life-Mars. Astrobiology 18, 1-27.

Infectious polymorphic toxins delivered by outer membrane exchange discriminate kin in myxobacteria

Myxobacteria are known for complex social behaviors including outer membrane exchange (OME), in which cells exchange large amounts of outer membrane lipids and proteins upon contact. The TraA cell surface receptor selects OME partners based on a variable domain. However, traA polymorphism alone is not sufficient to precisely discriminate kin. Here, we report a novel family of OME-delivered toxins that promote kin discrimination of OME partners. These SitA lipoprotein toxins are polymorphic and widespread in myxobacteria. Each sitA is associated with a cognate sitI immunity gene, and in some cases a sitB accessory gene. Remarkably, we show that SitA is transferred serially between target cells, allowing the toxins to move cell-to-cell like an infectious agent. Consequently, SitA toxins define strong identity barriers between strains and likely contribute to population structure, maintenance of cooperation, and strain diversification. Moreover, these results highlight the diversity of systems evolved to deliver toxins between bacteria.

Diversity of Serratia marcescens Strains Associated with Cucurbit Yellow Vine Disease in Georgia

Cucurbit yellow vine disease (CYVD), caused by the squash bug (Anasa tristis)-transmitted bacterium Serratia marcescens, was first identified in Oklahoma and Texas in 1988 and in Georgia in 2012. S. marcescens is a highly diverse species found in many ecological niches. In previous studies, CYVD strains of S. marcescens formed a closely related group separate from non-CYVD strains based on biological and molecular characterization techniques. Multilocus sequence analysis (MLSA) of six housekeeping genes and repetitive elements-based polymerase chain reaction (rep-PCR) using the BOX and ERIC primers were used to assess the genetic diversity of CYVD strains of S. marcescens collected in Georgia together with a strain from Texas and seven non-CYVD strains of S. marcescens. rep-PCR results revealed genetic diversity among CYVD strains while MLSA results showed a 100% similarity across the six loci for all but one of the CYVD strains, which differed at the icd locus by five polymorphisms. For both methods, CYVD strains clustered separately from nonplant-pathogenic S. marcescens strains and were most similar to a rice endophyte strain. One CYVD strain isolated from a squash bug shared genetic similarities with non-CYVD strains, and may be the result of a recombination event between CYVD and non-CYVD strains.

Local and Regional Diversity Reveals Dispersal Limitation and Drift as Drivers for Groundwater Bacterial Communities from a Fractured Granite Formation

Microorganisms found in terrestrial subsurface environments make up a large proportion of the Earth’s biomass. Biogeochemical cycles catalyzed by subsurface microbes have the potential to influence the speciation and transport of radionuclides managed in geological repositories. To gain insight on factors that constrain microbial processes within a formation with restricted groundwater flow we performed a meta-community analysis on groundwater collected from multiple discrete fractures underlying the Chalk River Laboratories site (located in Ontario, Canada). Bacterial taxa were numerically dominant in the groundwater. Although these were mainly uncultured, the closest cultivated representatives were from the phenotypically diverse Betaproteobacteria, Deltaproteobacteria, Bacteroidetes, Actinobacteria, Nitrospirae, and Firmicutes. Hundreds of taxa were identified but only a few were found in abundance (>1%) across all assemblages. The remainder of the taxa were low abundance. Within an ecological framework of selection, dispersal and drift, the local and regional diversity revealed fewer taxa within each assemblage relative to the meta-community, but the taxa that were present were more related than predicted by chance. The combination of dispersion at one phylogenetic depth and clustering at another phylogenetic depth suggest both niche (dispersion) and filtering (clustering) as drivers of local assembly. Distance decay of similarity reveals apparent biogeography of 1.5 km. Beta diversity revealed greater influence of selection at shallow sampling locations while the influences of dispersal limitation and randomness were greater at deeper sampling locations. Although selection has shaped each assemblage, the spatial scale of groundwater sampling favored detection of neutral processes over selective processes. Dispersal limitation between assemblages combined with local selection means the meta-community is subject to drift, and therefore, likely reflects the differential historical events that have influenced the current bacterial composition. Categorizing the study site into smaller regions of interest of more closely spaced fractures, or of potentially hydraulically connected fractures, might improve the resolution of an analysis to reveal environmental influences that have shaped these bacterial communities.

Interference Competition Among Household Strains of Pseudomonas

Bacterial species exhibit biogeographical patterns like those observed in larger organisms. The distribution of bacterial species is driven by environmental selection through abiotic and biotic factors as well dispersal limitations. We asked whether interference competition, a biotic factor, could explain variability in habitat use by Pseudomonas species in the human home. To answer this question, we screened almost 8000 directional, pairwise interactions between 89 Pseudomonas strains including members of the Pseudomonas aeruginosa (n = 29), Pseudomonas fluorescens (n = 21), and Pseudomonas putida (n = 39) species groups for the presence of killing. This diverse set of Pseudomonas strains includes those isolated from several different habitats within the home environment and includes combinations of strains that were isolated from different spatial scales. The use of this strain set not only allowed us to analyze the commonality and phylogenetic scale of interference competition within the genus Pseudomonas but also allowed us to investigate the influence of spatial scale on this trait. Overall, the probability of killing was found to decrease with increasing phylogenetic distance, making it unlikely that interference competition accounts for previously observed differential habitat use among Pseudomonas species and species groups. Strikingly, conspecific P. aeruginosa killing accounted for the vast majority of the observed killing, and this killing was found to differ across the habitat type and spatial scale of the strains' isolation. These data suggest that interference competition likely plays a large role in the within-species dynamics of P. aeruginosa but not other household Pseudomonas species.

Biogeography of sulfur-oxidizing Acidithiobacillus populations in extremely acidic cave biofilms

Extremely acidic (pH 0–1.5) Acidithiobacillus-dominated biofilms known as snottites are found in sulfide-rich caves around the world. Given the extreme geochemistry and subsurface location of the biofilms, we hypothesized that snottite Acidithiobacillus populations would be genetically isolated. We therefore investigated biogeographic relationships among snottite Acidithiobacillus spp. separated by geographic distances ranging from meters to 1000s of kilometers. We determined genetic relationships among the populations using techniques with three levels of resolution: (i) 16S rRNA gene sequencing, (ii) 16S–23S intergenic transcribed spacer (ITS) region sequencing and (iii) multi-locus sequencing typing (MLST). We also used metagenomics to compare functional gene characteristics of select populations. Based on 16S rRNA genes, snottites in Italy and Mexico are dominated by different sulfur-oxidizing Acidithiobacillus spp. Based on ITS sequences, Acidithiobacillus thiooxidans strains from different cave systems in Italy are genetically distinct. Based on MLST of isolates from Italy, genetic distance is positively correlated with geographic distance both among and within caves. However, metagenomics revealed that At. thiooxidans populations from different cave systems in Italy have different sulfur oxidation pathways and potentially other significant differences in metabolic capabilities. In light of those genomic differences, we argue that the observed correlation between genetic and geographic distance among snottite Acidithiobacillus populations is partially explained by an evolutionary model in which separate cave systems were stochastically colonized by different ancestral surface populations, which then continued to diverge and adapt in situ.

Actinobacterial Diversity in Volcanic Caves and Associated Geomicrobiological Interactions

Volcanic caves are filled with colorful microbial mats on the walls and ceilings. These volcanic caves are found worldwide, and studies are finding vast bacteria diversity within these caves. One group of bacteria that can be abundant in volcanic caves, as well as other caves, is Actinobacteria. As Actinobacteria are valued for their ability to produce a variety of secondary metabolites, rare and novel Actinobacteria are being sought in underexplored environments. The abundance of novel Actinobacteria in volcanic caves makes this environment an excellent location to study these bacteria. Scanning electron microscopy (SEM) from several volcanic caves worldwide revealed diversity in the morphologies present. Spores, coccoid, and filamentous cells, many with hair-like or knobby extensions, were some of the microbial structures observed within the microbial mat samples. In addition, the SEM study pointed out that these features figure prominently in both constructive and destructive mineral processes. To further investigate this diversity, we conducted both Sanger sequencing and 454 pyrosequencing of the Actinobacteria in volcanic caves from four locations, two islands in the Azores, Portugal, and Hawai'i and New Mexico, USA. This comparison represents one of the largest sequencing efforts of Actinobacteria in volcanic caves to date. The diversity was shown to be dominated by Actinomycetales, but also included several newly described orders, such as Euzebyales, and Gaiellales. Sixty-two percent of the clones from the four locations shared less than 97% similarity to known sequences, and nearly 71% of the clones were singletons, supporting the commonly held belief that volcanic caves are an untapped resource for novel and rare Actinobacteria. The amplicon libraries depicted a wider view of the microbial diversity in Azorean volcanic caves revealing three additional orders, Rubrobacterales, Solirubrobacterales, and Coriobacteriales. Studies of microbial ecology in volcanic caves are still very limited. To rectify this deficiency, the results from our study help fill in the gaps in our knowledge of actinobacterial diversity and their potential roles in the volcanic cave ecosystems.

Assessment of bioaerosol contamination (bacteria and fungi) in the largest urban wastewater treatment plant in the Middle East

Bioaerosol concentration was measured in wastewater treatment units in south of Tehran, the largest wastewater treatment plant in the Middle East. Active sampling was carried out around four operational units and a point as background. The results showed that the aeration tank with an average of 1016 CFU/m(3) in winter and 1973 CFU/m(3) in summer had the greatest effect on emission of bacterial bioaerosols. In addition, primary treatment had the highest impact on fungal emission. Among the bacteria, Micrococcus spp. showed the widest emission in the winter, and Bacillus spp. was dominant in summer. Furthermore, fungi such as Penicillium spp. and Cladosporium spp. were the dominant types in the seasons. Overall, significant relationship was observed between meteorological parameters and the concentration of bacterial and fungal aerosols.

Emerging spatial patterns in Antarctic prokaryotes

Recent advances in knowledge of patterns of biogeography in terrestrial eukaryotic organisms have led to a fundamental paradigm shift in understanding of the controls and history of life on land in Antarctica, and its interactions over the long term with the glaciological and geological processes that have shaped the continent. However, while it has long been recognized that the terrestrial ecosystems of Antarctica are dominated by microbes and their processes, knowledge of microbial diversity and distributions has lagged far behind that of the macroscopic eukaryote organisms. Increasing human contact with and activity in the continent is leading to risks of biological contamination and change in a region whose isolation has protected it for millions of years at least; these risks may be particularly acute for microbial communities which have, as yet, received scant recognition and attention. Even a matter apparently as straightforward as Protected Area designation in Antarctica requires robust biodiversity data which, in most parts of the continent, remain almost completely unavailable. A range of important contributing factors mean that it is now timely to reconsider the state of knowledge of Antarctic terrestrial prokaryotes. Rapid advances in molecular biological approaches are increasingly demonstrating that bacterial diversity in Antarctica may be far greater than previously thought, and that there is overlap in the environmental controls affecting both Antarctic prokaryotic and eukaryotic communities. Bacterial dispersal mechanisms and colonization patterns remain largely unaddressed, although evidence for regional evolutionary differentiation is rapidly accruing and, with this, there is increasing appreciation of patterns in regional bacterial biogeography in this large part of the globe. In this review, we set out to describe the state of knowledge of Antarctic prokaryote diversity patterns, drawing analogy with those of eukaryote groups where appropriate. Based on our synthesis, it is clear that spatial patterns of Antarctic prokaryotes can be unique at local scales, while the limited evidence available to date supports the group exhibiting overall regional biogeographical patterns similar to the eukaryotes. We further consider the applicability of the concept of “functional redundancy” for the Antarctic microbial community and highlight the requirements for proper consideration of their important and distinctive roles in Antarctic terrestrial ecosystems.

Biogeography and evolution of Thermococcus isolates from hydrothermal vent systems of the Pacific

Thermococcus is a genus of hyperthermophilic archaea that is ubiquitous in marine hydrothermal environments growing in anaerobic subsurface habitats but able to survive in cold oxygenated seawater. DNA analyses of Thermococcus isolates were applied to determine the relationship between geographic distribution and relatedness focusing primarily on isolates from the Juan de Fuca Ridge and South East Pacific Rise. Amplified fragment length polymorphism (AFLP) analysis and multilocus sequence typing (MLST) were used to resolve genomic differences in 90 isolates of Thermococcus, making biogeographic patterns and evolutionary relationships apparent. Isolates were differentiated into regionally endemic populations however there was also evidence in some lineages of cosmopolitan distribution. The biodiversity identified in Thermococcus isolates and presence of distinct lineages within the same vent site suggests the utilization of varying ecological niches in this genus. In addition to resolving biogeographic patterns in Thermococcus, this study has raised new questions about the closely related Pyrococcus genus. The phylogenetic placement of Pyrococcus type strains shows the close relationship between Thermococcus and Pyrococcus and the unresolved divergence of these two genera.

Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms

BACKGROUND

High-throughput sequencing technologies are lifting major limitations to molecular-based ecological studies of eukaryotic microbial diversity, but analyses of the resulting millions of short sequences remain a major bottleneck for these approaches. Here, we introduce the analytical and statistical framework of sequence similarity networks, increasingly used in evolutionary studies and graph theory, into the field of ecology to analyze novel pyrosequenced V4 small subunit rDNA (SSU-rDNA) sequence data sets in the context of previous studies, including SSU-rDNA Sanger sequence data from cultured ciliates and from previous environmental diversity inventories.

RESULTS

Our broadly applicable protocol quantified the progress in the description of genetic diversity of ciliates by environmental SSU-rDNA surveys, detected a fundamental historical bias in the tendency to recover already known groups in these surveys, and revealed substantial amounts of hidden microbial diversity. Moreover, network measures demonstrated that ciliates are not globally dispersed, but are structured by habitat and geographical location at intermediate geographical scale, as observed for bacteria, plants, and animals.

CONCLUSIONS

Currently available 'universal' primers used for local in-depth sequencing surveys provide little hope to exhaust the significantly higher ciliate (and most likely microbial) diversity than previously thought. Network analyses such as presented in this study offer a promising way to guide the design of novel primers and to further explore this vast and structured microbial diversity.

Comparative genomics of the marine bacterial genus Glaciecola reveals the high degree of genomic diversity and genomic characteristic for cold adaptation

To what extent the genomes of different species belonging to one genus can be diverse and the relationship between genomic differentiation and environmental factor remain unclear for oceanic bacteria. With many new bacterial genera and species being isolated from marine environments, this question warrants attention. In this study, we sequenced all the type strains of the published species of Glaciecola, a recently defined cold-adapted genus with species from diverse marine locations, to study the genomic diversity and cold-adaptation strategy in this genus.The genome size diverged widely from 3.08 to 5.96 Mb, which can be explained by massive gene gain and loss events. Horizontal gene transfer and new gene emergence contributed substantially to the genome size expansion. The genus Glaciecola had an open pan-genome. Comparative genomic research indicated that species of the genus Glaciecola had high diversity in genome size, gene content and genetic relatedness. This may be prevalent in marine bacterial genera considering the dynamic and complex environments of the ocean. Species of Glaciecola had some common genomic features related to cold adaptation, which enable them to thrive and play a role in biogeochemical cycle in the cold marine environments.

Distance-decay and taxa-area relationships for bacteria, archaea and methanogenic archaea in a tropical lake sediment

The study of of the distribution of microorganisms through space (and time) allows evaluation of biogeographic patterns, like the species-area index (z). Due to their high dispersal ability, high reproduction rates and low rates of extinction microorganisms tend to be widely distributed, and they are thought to be virtually cosmopolitan and selected primarily by environmental factors. Recent studies have shown that, despite these characteristics, microorganisms may behave like larger organisms and exhibit geographical distribution. In this study, we searched patterns of spatial diversity distribution of bacteria and archaea in a contiguous environment. We collected 26 samples of a lake sediment, distributed in a nested grid, with distances between samples ranging from 0.01 m to 1000 m. The samples were analyzed using T-RFLP (Terminal restriction fragment length polymorphism) targeting mcrA (coding for a subunit of methyl-coenzyme M reductase) and the genes of Archaeal and Bacterial 16S rRNA. From the qualitative and quantitative results (relative abundance of operational taxonomic units) we calculated the similarity index for each pair to evaluate the taxa-area and distance decay relationship slopes by linear regression. All results were significant, with mcrA genes showing the highest slope, followed by Archaeal and Bacterial 16S rRNA genes. We showed that the microorganisms of a methanogenic community, that is active in a contiguous environment, display spatial distribution and a taxa-area relationship.

Biogeographic patterns in ocean microbes emerge in a neutral agent-based model

A key question in ecology and evolution is the relative role of natural selection and neutral evolution in producing biogeographic patterns. We quantify the role of neutral processes by simulating division, mutation, and death of 100,000 individual marine bacteria cells with full 1 million-base-pair genomes in a global surface ocean circulation model. The model is run for up to 100,000 years and output is analyzed using BLAST (Basic Local Alignment Search Tool) alignment and metagenomics fragment recruitment. Simulations show the production and maintenance of biogeographic patterns, characterized by distinct provinces subject to mixing and periodic takeovers by neighbors (coalescence), after which neutral evolution reestablishes the province and the patterns reorganize. The emergent patterns are substantial (e.g., down to 99.5% DNA identity between North and Central Pacific provinces) and suggest that microbes evolve faster than ocean currents can disperse them. This approach can also be used to explore environmental selection.

Patterns and processes of microbial community assembly

Recent research has expanded our understanding of microbial community assembly. However, the field of community ecology is inaccessible to many microbial ecologists because of inconsistent and often confusing terminology as well as unnecessarily polarizing debates. Thus, we review recent literature on microbial community assembly, using the framework of Vellend (Q. Rev. Biol. 85:183-206, 2010) in an effort to synthesize and unify these contributions. We begin by discussing patterns in microbial biogeography and then describe four basic processes (diversification, dispersal, selection, and drift) that contribute to community assembly. We also discuss different combinations of these processes and where and when they may be most important for shaping microbial communities. The spatial and temporal scales of microbial community assembly are also discussed in relation to assembly processes. Throughout this review paper, we highlight differences between microbes and macroorganisms and generate hypotheses describing how these differences may be important for community assembly. We end by discussing the implications of microbial assembly processes for ecosystem function and biodiversity.

Ecological diversification of Vibrio fischeri serially passaged for 500 generations in novel squid host Euprymna tasmanica

Vibrio fischeri isolated from Euprymna scolopes (Cephalopoda: Sepiolidae) was used to create 24 lines that were serially passaged through the non-native host Euprymna tasmanica for 500 generations. These derived lines were characterized for biofilm formation, swarming motility, carbon source utilization, and in vitro bioluminescence. Phenotypic assays were compared between "ES" (E. scolopes) and "ET" (E. tasmanica) V. fischeri wild isolates to determine if convergent evolution was apparent between E. tasmanica evolved lines and ET V. fischeri. Ecological diversification was observed in utilization of most carbon sources examined. Convergent evolution was evident in motility, biofilm formation, and select carbon sources displaying hyperpolymorphic usage in V. fischeri. Convergence in bioluminescence (a 2.5-fold increase in brightness) was collectively evident in the derived lines relative to the ancestor. However, dramatic changes in other properties--time points and cell densities of first light emission and maximal light output and emergence of a lag phase in growth curves of derived lines--suggest that increased light intensity per se was not the only important factor. Convergent evolution implies that gnotobiotic squid light organs subject colonizing V. fischeri to similar selection pressures. Adaptation to novel hosts appears to involve flexible microbial metabolism, establishment of biofilm and swarmer V. fischeri ecotypes, and complex changes in bioluminescence. Our data demonstrate that numerous alternate fitness optima or peaks are available to V. fischeri in host adaptive landscapes, where novel host squids serve as habitat islands. Thus, V. fischeri founder flushes occur during the initiation of light organ colonization that ultimately trigger founder effect diversification.

Life in extreme environments: microbial diversity in Great Salt Lake, Utah

Great Salt Lake (GSL) represents one of the world's most hypersaline environments. In this study, the archaeal and bacterial communities at the North and South arms of the lake were surveyed by cloning and sequencing the 16S rRNA gene. The sampling locations were chosen for high salt concentration and the presence of unique environmental gradients, such as petroleum seeps and high sulfur content. Molecular techniques have not been systematically applied to this extreme environment, and thus the composition and the genetic diversity of microbial communities at GSL remain mostly unknown. This study led to the identification of 58 archaeal and 42 bacterial operational taxonomic units. Our phylogenetic and statistical analyses displayed a high biodiversity of the microbial communities in this environment. In this survey, we also showed that the majority of the 16S rRNA gene sequences within the clone library were distantly related to previously described environmental halophilic archaeal and bacterial taxa and represent novel phylotypes.

Molecular phylogenetics and temporal diversification in the genus Aeromonas based on the sequences of five housekeeping genes

Several approaches have been developed to estimate both the relative and absolute rates of speciation and extinction within clades based on molecular phylogenetic reconstructions of evolutionary relationships, according to an underlying model of diversification. However, the macroevolutionary models established for eukaryotes have scarcely been used with prokaryotes. We have investigated the rate and pattern of cladogenesis in the genus Aeromonas (γ-Proteobacteria, Proteobacteria, Bacteria) using the sequences of five housekeeping genes and an uncorrelated relaxed-clock approach. To our knowledge, until now this analysis has never been applied to all the species described in a bacterial genus and thus opens up the possibility of establishing models of speciation from sequence data commonly used in phylogenetic studies of prokaryotes. Our results suggest that the genus Aeromonas began to diverge between 248 and 266 million years ago, exhibiting a constant divergence rate through the Phanerozoic, which could be described as a pure birth process.

Fungal endophytes associated with three South American Myrtae (Myrtaceae) exhibit preferences in the colonization at leaf level

Fungal endophytes associated with Myrtaceae from Brazil and Argentina were isolated at three levels of nesting: leaf, individual host trees, and site collection. The alternating logistic regression (ALR) was used to model the data because it offers a computationally convenient method for fitting regression structures involving large clusters. The objectives of this study were to determine: (i) whether the colonization pattern is influenced by environmental variables, (ii) if there is some leaf part they prefer to colonize; (iii) if there is some fungal endophyte aggregation between hierarchical levels; (iv) what the distance effect is on the fungal association. The environmental variables were statistically significant only for Xylaria, i.e., when the elevation and water precipitation increase and the temperature decreases, the odds ratio of finding another fungal endophyte of that genus previously found increases. Sordariomycetes, Xylariales, and Xylaria exhibited leaf fragment preference to petiole and tip. Fungal endophytes showed association within leaf. The horizontal transmission mode and the dispersal limitation may explain this association at the leaf level. Moreover, our results suggest that when a fungal endophyte infects a leaf or host tree individual, the odds ratio of dispersal inside them is greater.

Frequent recombination shapes the epidemic population structure of Planktothrix (Cyanoprokaryota) in Italian subalpine lakes

The planktonic genus Planktothrix, as other cyanobacteria, shows signals of both homologous and nonhomologous recombination. However, the frequency of recombination and its effect on Planktothrix population structuring is unknown. We isolated 290 Planktothrix strains from seven neighboring lakes in the subalpine Italian region and analyzed these using multilocus sequence typing. Four of six loci analyzed were polymorphic, resulting in 20 distinct multilocus genotypes. Association indices among alleles at different loci were suggestive of an "epidemic population structure," resulting from an explosive (and temporary) dominance of one genotype against a panmictic background. ClonalFrame analyses supported this view by detecting: (i) three major clades affected by three distinct recombination events, (ii) a recombination rate about equal to the mutation rate, and (iii) the fact that recombination had an impact on introducing molecular diversity more than double the mutation rate. Furthermore, analysis of molecular variance over an annual cycle in three of seven lakes revealed that both local clonal expansion and recombination processes affected among-lake diversity. Our observations suggest that recombination affects microevolution of Planktothrix and that an epidemic structure can emerge in populations of this genus.

Nodule morphology, symbiotic specificity and association with unusual rhizobia are distinguishing features of the genus Listia within the Southern African crotalarioid clade Lotononis s.l

BACKGROUND AND AIMS

The legume clade Lotononis sensu lato (s.l.; tribe Crotalarieae) comprises three genera: Listia, Leobordea and Lotononis sensu stricto (s.s.). Listia species are symbiotically specific and form lupinoid nodules with rhizobial species of Methylobacterium and Microvirga. This work investigated whether these symbiotic traits were confined to Listia by determining the ability of rhizobial strains isolated from species of Lotononis s.l. to nodulate Listia, Leobordea and Lotononis s.s. hosts and by examining the morphology and structure of the resulting nodules.

METHODS

Rhizobia were characterized by sequencing their 16S rRNA and nodA genes. Nodulation and N2 fixation on eight taxonomically diverse Lotononis s.l. species were determined in glasshouse trials. Nodules of all hosts, and the process of infection and nodule initiation in Listia angolensis and Listia bainesii, were examined by light microscopy.

KEY RESULTS

Rhizobia associated with Lotononis s.l. were phylogenetically diverse. Leobordea and Lotononis s.s. isolates were most closely related to Bradyrhizobium spp., Ensifer meliloti, Mesorhizobium tianshanense and Methylobacterium nodulans. Listia angolensis formed effective nodules only with species of Microvirga. Listia bainesii nodulated only with pigmented Methylobacterium. Five lineages of nodA were found. Listia angolensis and L. bainesii formed lupinoid nodules, whereas nodules of Leobordea and Lotononis s.s. species were indeterminate. All effective nodules contained uniformly infected central tissue. Listia angolensis and L. bainesii nodule initials occurred on the border of the hypocotyl and along the tap root, and nodule primordia developed in the outer cortical layer. Neither root hair curling nor infection threads were seen.

CONCLUSIONS

Two specificity groups occur within Lotononis s.l.: Listia species are symbiotically specific, while species of Leobordea and Lotononis s.s. are generally promiscuous and interact with rhizobia of diverse chromosomal and symbiotic lineages. The seasonally waterlogged habitat of Listia species may favour the development of symbiotic specificity.

Dissecting the deep biosphere: retrieving authentic microbial communities from packer-isolated deep crystalline bedrock fracture zones

Deep fracture zones in Finnish crystalline bedrock have been isolated for long, the oldest fluids being tens of millions of years old. To accurately measure the native microbial diversity in fracture-zone fluids, water samples were obtained by isolating the borehole fraction spanning a deep subsurface aquifer fracture zone with inflatable packers (500 and 967 m) or by pumping fluids directly from the fracture zone. Sampling frequency was examined to establish the time required for the space between packers to be flushed and replaced by indigenous fracture fluids. Chemical parameters of the fluid were monitored continuously, and samples were taken at three points during the flushing process. Microbial communities were characterized by comparison of 16S ribosomal genes and transcripts and quantification of dsrB (dissimilatory sulfate reduction) gene. Results suggest that fracture-zones host microbial communities with fewer cells and lower diversity than those in the drill hole prior to flushing. In addition, each fracture zone showed a community composition distinct from that inhabiting the drill hole at corresponding depth. The highest diversity was detected from the 967-m fracture zone. We conclude that the applied packer method can successfully isolate and sample authentic microbial fracture-zone communities of deep bedrock environments.