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bioRxiv2021

Metacommunity analyses show increase in ecological specialisation throughout the Ediacaran

The first animals appear during the late Ediacaran (572 - 541 Ma); an initial diversity increase was followed by a drop, interpreted as catastrophic mass extinction. We investigate the processes underlying these changes using the "Elements of Metacommunity Structure" framework. The oldest metacommunity was characterized by taxa with wide environmental tolerances, and limited specialisation and inter-taxa interactions. Structuring increased in the middle metacommunity, with groups of taxa sharing synchronous responses to environmental gradients, aggregating into distinct communities. This pattern strengthened in the youngest metacommunity, with communities showing strong environmental segregation and depth structure. Thus, metacommunity structure increased in complexity, with increased specialisation and resulting competitive exclusion, not a catastrophic environmental disaster, leading to diversity loss in the terminal Ediacaran, revealing that the complex eco-evolutionary dynamics associated with Cambrian diversification were established in the Ediacaran.

paleontology↗

bioRxiv2021

Association between quinolone use in food animals and gonococcal resistance to ciprofloxacin: an ecological study

BackgroundConcentrations of fluoroquinolones up to 200-fold lower than the MIC have been shown to be able to select for antimicrobial resistance in E. coli and Salmonella spp. (the minimum selection concentration - MSC). We aimed to i) establish what the ciprofloxacin MSC is for Neisseria gonorrhoeae and ii) Assess at a country level if the prevalence of gonococcal ciprofloxacin resistance is associated with the concentration of quinolones used in food animal production (an important determinant of long-term low dose ciprofloxacin exposures in humans). Methodsi). To assess if sub-inhibitory ciprofloxacin concentrations could select for de novo generated resistant mutants, susceptible WHO-P was serially passaged at 1, 1/10, 1/100 and 1/1000 of the ciprofloxacin MIC of WHO-P (0.004mg/L) on GC agar plates. ii) Spearmans correlation was used to assess the association between the prevalence of ciprofloxacin resistance in N. gonorrhoeae and the two independent variables - quinolone use for animals and quinolone consumption by humans. ResultsCiprofloxacin concentrations as low as 1/1000 of the MIC of WHO-P were able to select for ciprofloxacin resistance. The prevalence of ciprofloxacin resistance in N. gonorrhoeae was positively associated with quinolone use for food animals ({rho}=0.47; P=0.004; N=34). ConclusionFurther individual level research is required to assess if low doses of ciprofloxacin from ingested foodstuffs are able to select for ciprofloxacin resistance in N. gonorrhoeae and other species.

microbiology↗

bioRxiv2021

A marginal habitat, but not a sink: Ecological genetics reveal a diversification hotspot for marine invertebrates in the brackish Baltic Sea

AimEnvironmental gradients have emerged as important barriers structuring populations and species distributions. We set out to test whether a strong salinity gradient from marine to brackish, represented in a marginal northern European sea, should be considered a diversification hotspot or a population sink, and to identify life history traits that correlate with either evolutionary trajectory. LocationThe Baltic Sea, the North Sea and their transition zone. MethodsWe accumulated mitochondrial cytochrome oxidase subunit 1 sequence data and data on the distribution, salinity tolerance and life history for 28 species belonging to the Cnidaria, Crustacea, Echinodermata, Mollusca, Polychaeta and Gastrotricha, including seven non-native species. We calculated measures of genetic diversity and differentiation across the environmental gradient, coalescent times and migration rates between North and Baltic Sea populations, and analysed correlations between genetic and life history data. ResultsThe majority of investigated species is either genetically differentiated and/or is adapted to the lower salinity conditions of the Baltic Sea. Moreover, the species exhibiting population structure have a range of patterns of genetic diversity in comparison to the North Sea, from lower in the Baltic Sea to higher in the Baltic Sea, or equally diverse in North and Baltic Sea. Main conclusionsOur results indicate that the Baltic Sea should be considered a diversification hotspot: The diversity of genetic patterns points towards independent trajectories in the Baltic compared to the North Sea. At the same time, we found limited evidence for the traditional scenario of the Baltic Sea as a population sink with lower diversity and strong gene flow. The North Sea - Baltic Sea region provides a unique setting to study evolutionary adaptation during colonization processes at different stages by jointly considering native and non-native species.

evolutionary biology↗

bioRxiv2021

Convergent adaptation and ecological speciation result from unique genomic mechanisms in sympatric extremophile fishes

The evolution of independent lineages along replicated environmental gradients frequently results in convergent adaptation, yet the degree to which convergence is present across multiple levels of biological organization is often unclear. Additionally, inherent biases associated with shared ancestry and variation in selective regimes across geographic replicates often pose challenges for confidently identifying patterns of convergence. We investigated a system in which three species of poeciliid fishes sympatrically occur in a toxic spring rich in hydrogen sulfide (H2S) and an adjacent nonsulfidic stream to examine patterns of adaptive evolution across levels of biological organization. We found convergence in morphological and physiological traits and genome-wide patterns of gene expression among all three species. In addition, there were shared signatures of selection on genes encoding H2S toxicity targets in the mitochondrial genomes of each species. However, analyses of nuclear genomes revealed neither evidence for substantial genomic islands of divergence around genes involved in H2S toxicity and detoxification nor substantial congruence of strongly differentiated regions across population pairs. These non-convergent, heterogenous patterns of genomic divergence may indicate that sulfide tolerance is highly polygenic, with shared allele frequency shifts present at many loci with small effects along the genome. Alternatively, H2S tolerance may involve substantial genetic redundancy, with non-convergent lineage-specific variation at multiple loci along the genome underpinning similar changes in phenotypes and gene expression. Overall, we demonstrate variability in the extent of convergence across organizational levels and highlight the challenges of linking patterns of convergence across scales.

evolutionary biology↗

bioRxiv2021

Ecology and transmission of a dengue virus serotype 4 identified in wild Aedes aegypti in Florida

1Dengue virus is the most prevalent mosquito-borne virus, causing approximately 390 million infections and 25,000 deaths per year. Aedes aegypti, the primary mosquito vector of dengue virus, is well established throughout the state of Florida, USA. Autochthonous transmission of dengue virus to humans in Florida has been increasing since 2009, alongside consistent importation of dengue cases. However, most cases of first infection with dengue are asymptomatic and the virus can be maintained in mosquito populations, complicating surveillance and leading to an underestimation of disease risk. Metagenomic sequencing of Aedes aegypti mosquitoes in Manatee County, Florida revealed the presence of dengue virus serotype 4 (DENV-4) genomes in mosquitoes from multiple trapping sites over 2 years, in the absence of a human DENV-4 index case and even though a locally acquired case of DENV-4 has never been reported in Florida. This finding suggested that: i) DENV-4 may circulate amongst humans undetected, ii) the virus was being maintained in the mosquito population, or iii) the detected complete genome sequence may not represent a viable virus. This study demonstrates that an infectious clone generated from the Manatee County DENV-4 (DENV-4M) sequence is capable of infecting mammalian and insect tissue culture systems, as well as adult female Aedes aegypti mosquitoes when fed in a blood meal. However, the virus is subject to a dose dependent infection barrier in mosquitoes, and has a kinetic delay compared to a phylogenetically related wild-type (WT) control virus from a symptomatic child, DENV-4H (strain Homo sapiens/Haiti-0075/2015, GenBank accession MK514144.1). DENV-4M disseminates from the midgut to the ovary and saliva at 14 days post-infection. Viral RNA was also detectable in the adult female offspring of DENV-4M infected mosquitoes. These results demonstrate that the virus is capable of infecting vector mosquitoes, is transmissible by bite, and is vertically transmitted, indicating a mechanism for maintenance in the environment without human-mosquito transmission. These findings suggest undetected human-mosquito transmission and/or long-term maintenance of the virus in the mosquito population is occurring in Florida, and underscore the importance of proactive surveillance for viruses in mosquitoes. Graphical AbstractIn order to better assess the public health risk posed by a detection of DENV-4 RNA in Manatee County, FL Aedes aegypti, we produced an infectious clone using the sequence from the wild-caught mosquitoes and characterized it via laboratory infections of mosquitoes and mosquito tissues.

microbiology↗

bioRxiv2021

Protozoan predation drives adaptive divergence in Pseudomonas fluorescens SBW25; ecology meets experimental evolution.

Protozoan predators can affect the structure of bacterial communities, but investigations of how predation might influence bacterial evolution and antagonistic behaviours are scarce. Here, we performed a 20-day predator-prey evolution experiment on solid media to investigate the effect of continuous protozoan predation on bacterial traits using Pseudomonas fluorescens SBW25 as prey and Naegleria gruberi as an amoeboid predator. We observed the divergence of colony morphotypes coincident with an increase in bacterial grazing resistance and relative prey fitness in selected bacterial isolates. When subjected to these resistant prey, N. gruberi show reduced activity (increased encystment) and limited replication. An investigation of the mutations responsible for predation resistance reveals mutations in wspF and amrZ genes, affecting biofilm formation and motility. The bacterial mutants in the wspF gene successfully colonise the air-liquid interface and produce robust cellulose biofilms that prevent predation. The mutation in the amrZ mutant withstands predation but this variant produces low levels of cellulose and limited swarming motility. Our findings suggest that protozoan predation can profoundly influence the course of genetic and phenotypic evolution in a short period.

evolutionary biology↗

bioRxiv2021

Is the genomics cart before the restoration ecology horse? Insights from qualitative interviews and trends from the literature

Harnessing new technologies is vital to achieve global imperatives to restore degraded ecosystems. We explored the potential of genomics as one such tool. We aimed to understand barriers hindering the uptake of genomics, and how to overcome them, via exploratory interviews with leading scholars in both restoration and its sister discipline of conservation - a discipline that has successfully leveraged genomics. We also conducted an examination of research trends to explore some insights that emerged from the interviews, including publication trends that have used genomics to address restoration and conservation questions. Our qualitative findings revealed varied perspectives in harnessing genomics. For example, scholars in restoration without genomics experience felt genomics was over-hyped. Scholars with genomics experience emphatically emphasised the need to proceed cautiously in using genomics in restoration. Both genomics-experienced and less-experienced scholars called for case studies to demonstrate the benefits of genomics in restoration. These qualitative data contrasted with our examination of research trends, which revealed 70 restoration genomics studies, particularly studies using environmental DNA as a monitoring tool. We provide a roadmap to facilitate the uptake of genomics into restoration, to help the restoration sector meet the monumental task of restoring huge areas to biodiverse and functional ecosystems.

scientific communication and education↗

bioRxiv2021

Mechanisms of ecological divergence with gene flow in a reef-building coral on an isolated atoll in Western Australia

Understanding the mechanisms driving phenotypic variation in traits facing intensified selection from climate change is a crucial step in developing effective conservation and restoration initiatives. This is particularly true for reef-building corals, which are among the most vulnerable to climate change and are in dramatic decline globally. At the Rowley Shoals in Western Australia, the prominent reef flat becomes exposed on low tide and the stagnant water in the shallow atoll lagoons heats up, creating a natural laboratory for characterising the mechanisms that control phenotypic responses to different environments. We combined whole genome re-sequencing, common garden heat stress experiments, transcriptome-wide gene expression analyses, and symbiont metabarcoding to explore the mechanisms that facilitate survival in contrasting habitat conditions. Our data show that, despite high gene flow between habitats, spatially varying selection drives subtle shifts in allele frequencies at hundreds of loci. These changes were concentrated into several islands of divergence spanning hundreds of SNPs that showed strong linkage disequilibrium and were associated with a coordinated increase in minor allele frequencies in corals taken from the lagoon habitat, where the range of environmental conditions is greatest. Common garden heat stress assays showed individuals from the lagoon exhibited higher bleaching resistance than colonies from the reef slope, and RNAseq identified pronounced physiological differences between the corals from the two habitats, primarily associated with molecular pathways including cell signalling, ion transport and metabolism. Despite the pronounced physioloigical and environmental differences between habitats, metabarcoding of the Symbiodiniaceae ITS2 region revealed all colonies to be associated exclusively with the genus Cladocopium, with no detectable differences between habitats. This study contributes to the growing number of studies documenting the complex mechanisms that facilitate coral survival in extreme environments, and showcases the utility of combining multiple sequencing techniques to unravel complex climate-related traits.

genomics↗

bioRxiv2021

Predicted responses to selection across the climatic range of a rainforest Drosophila without local adaptation: environmental variation limits trait divergence along ecological gradients

Evolutionary responses to environmental change require heritable variation in traits under selection. Both heritability and selection vary with the environment, and may also covary, so environmental variation can affect evolutionary rates. However, simultaneous estimates of heritability and selection across environmental gradients in the field are rare. We estimated environmental variation in selection on three traits (cold tolerance, heat tolerance, and wing size) of the rainforest fruitfly Drosophila birchii. We transplanted flies in cages along two elevational gradients in north-east Queensland, Australia, and calculated the genetic covariance of trait values with fitness (productivity in cages) at each site. For wing size, we estimated heritability at each site from the correlation between field-reared offspring and their laboratory-reared relatives. We used estimates of selection and heritability to predict selection responses along the elevation gradients, and compared these with trait variation observed in flies sourced from populations at elevational extremes. We found evidence for divergent selection on cold tolerance across elevation at one gradient. Heritability of wing size was highest at gradient ends, and the size of the predicted response to selection on this trait increased with elevation. However, the direction of selection varied, even among adjacent sites, making such selection unlikely to cause divergence of this trait with elevation. None of the traits differed between populations from elevational extremes at either gradient. Variation in the strength and direction of selection over small spatial scales, as well as in time, may explain why predicted responses to selection are often not seen in natural populations.

evolutionary biology↗

bioRxiv2021

Chemistry, Taxonomy and Ecology of the potentially chimpanzee-dispersed Vepris teva sp.nov. (Rutaceae) of coastal thicket in the Congo Republic

Continuing a survey of the chemistry of species of the largely continental African genus Vepris, we investigate a species previously referred to as Vepris sp. 1 of Congo. From the leaves of Vepris sp. 1 we report six compounds. The compounds were three furoquinoline alkaloids, kokusaginine (1), maculine (2), and flindersiamine (3), two acridone alkaloids, arborinine (4)and 1-hydroxy-3-methoxy-10-methylacridone (5), and the triterpenoid, {beta}-amyrin (6). Compounds 1-4 are commonly isolated from other Vepris species, compound 5 has been reported before once, from Malagasy Vepris pilosa, while this is the first report of {beta}-amyrin from Vepris. This combination of compounds has never before been reported from any species of Vepris. We test the hypothesis that Vepris sp.1 is new to science and formally describe it as Vepris teva, unique in the genus in that the trifoliolate leaves are subsessile, with the median petiolule far exceeding the petiole in length. Similar fleshy-leathery 4-locular syncarpous fruits are otherwise only known in the genus in Vepris glaberrima (formerly the monotypic genus Oriciopsis Engl.), a potential sister species, but requiring further investigation to confirm this phylogenetic position. We briefly characterise the unusual and poorly documented Atlantic coast equatorial ecosystem, where Vepris teva is restricted to evergreen thicket on white sand, unusual in a genus usually confine to evergreen forest. This endemic-rich ecosystem with a unique amphibian as well as plants, extends along the coastline from the mouth of the Congo River to southern Rio Muni, a distance of about 1000 km, traversing five countries. We map and illustrate Vepris teva and assess its extinction risk as Endangered (EN B1ab(iii)+B2ab(iii)) using the IUCN standard. Only three locations are known, and threats include port and oil refinery construction and associated activities, with only one protected location, the Jane Goodall Institutes Tchimpounga Reserve. Initial evidence indicates that the seeds of Vepris teva are dispersed by chimpanzees, previously unreported in the genus

plant biology↗

bioRxiv2021

Chromosome-scale genome assembly of the brown anole (Anolis sagrei), a model species for evolution and ecology

Rapid technological improvements are democratizing access to high quality, chromosome-scale genome assemblies. No longer the domain of only the most highly studied model organisms, now non-traditional and emerging model species can be genome-enabled using a combination of sequencing technologies and assembly software. Consequently, old ideas built on sparse sampling across the tree of life have recently been amended in the face of genomic data drawn from a growing number of high-quality reference genomes. Arguably the most valuable are those long-studied species for which much is already known about their biology; what many term emerging model species. Here, we report a new, highly complete chromosome-scale genome assembly for the brown anole, Anolis sagrei - a lizard species widely studied across a variety of disciplines and for which a high-quality reference genome was long overdue.

genomics↗

bioRxiv2021

Recurrent urinary tract infection and estrogen shape the taxonomic ecology and functional potential of the postmenopausal urobiome

Community-acquired urinary tract infection (UTI) is among the most common bacterial infections observed in humans. Postmenopausal women are a rapidly growing and underserved demographic group who are severely affected by recurrent UTI (rUTI) with a >50% recurrence rate. In this population, rUTI can persist for years, reducing quality of life and imposing a significant healthcare burden. rUTI is most often treated by antibiotics, but development of antibiotic resistance and allergy limit therapeutic options. The female urinary microbiome (urobiome) has been identified as a key component of the urogenital environment. However, compositional and functional changes in the urobiome underlying rUTI susceptibility in postmenopausal women are not well understood. Here, we used a controlled, cross-sectional cohort of postmenopausal women, to interrogate changes in urobiome structure and function linked to rUTI susceptibility by whole genome metagenomic sequencing (WGMS), advanced urine culture, estrogen metabolite profiling, and antibiotic sensitivity testing. Overall, we detected 276 bacterial, archaeal, and fungal species representing 106 genera. We find a putative commensal population consisting of species known to protect against bacterial vaginosis, such as Lactobacillus crispatus, within the urobiome of postmenopausal women who do not experience UTI. Integration of clinical metadata detected an almost exclusive enrichment of lactobacilli, including L. crispatus and L. vaginalis, in women taking estrogen hormone therapy (EHT). Integrating quantitative metabolite profiling of urinary estrogens with WGMS, we observed robust correlations between urobiome taxa, such as Bifidobacterium breve and L. crispatus, and urinary estrogen conjugate concentrations in women with no history of UTI that were absent in women with rUTI history. We further used functional metagenomic profiling and patient-derived isolate phenotyping to identify microbial metabolic pathways, antimicrobial resistance genes (ARGs), and clinically relevant antimicrobial resistance phenotypes enriched between disease-states. Our data indicate that distinct urobiome metabolic and ARG signatures are associated with current rUTI status and history. Importantly, we observed that rUTI history leaves an imprint of enriched ARGs even in women not currently experiencing UTI. Taken together, our data suggests that rUTI history and estrogen strongly shape the functional and taxonomic composition of the urobiome in postmenopausal women.

microbiology↗

bioRxiv2021

Ecological validity of masking release with speech-like stimuli

The relevance of masking release by comodulation and interaural phase difference (IPD) for speech perception is still unclear. We used speech-like stimuli to link spectro-temporal properties of formants with masking release. The stimuli comprised a tone and three masker bands centered at formant frequencies F1, F2, and F3 derived from a consonant-vowel (/gu/, /fu/, and /pu/). The target was a diotic or dichotic frequency-modulated tone following F2 trajectories. Results showed no statistically significant comodulation masking release (CMR), while the binaural masking level difference (BMLD) was comparable to previous findings. The data suggest that factors other than comodulation may play a dominant role in grouping frequency components in speech.

animal behavior and cognition↗

bioRxiv2021

Parental control: ecology drives plasticity in parental response to offspring signals

Different bird species have completely different parent-offspring interactions. When food is plentiful, the chicks that are begging the loudest are fed the most. When food is scarce, bird species instead feed the largest offspring. While this variation could be due to parents responding to signalling differently based on food availability, it could equally be due to offspring adjusting their behaviour, or to variation in information availability. We tested between these competing explanations experimentally, by manipulating food availability in a population of wild great tits, Parus major, while standardising offspring behaviour and size. We found that when food was more plentiful, parents were: (1) more likely to preferentially feed the chicks that were begging the most; and (2) less likely to preferentially feed larger chicks. In addition, we consistently found these same patterns, in a meta-analysis across 57 bird species. Overall, our results suggest that parents have more control over food distribution than offspring do, and that they flexibly adjust how they respond to both offspring signals and cues of offspring quality in response to food availability. Consequently, depending upon environmental conditions, predictably different signalling systems are favoured.

animal behavior and cognition↗

bioRxiv2021

Adapting to novel environments together: evolutionary and ecological correlates of the bacterial microbiome of the worlds largest cavefish diversification

The symbiosis between a host and its microbiome is essential for host fitness, and this association is a consequence of the hosts physiology and habitat. Sinocyclocheilus, the largest cavefish diversification of the world, an emerging multi-species model system for evolutionary novelty, provides an excellent opportunity for examining correlates of host evolutionary history, habitat, and gut-microbial community diversity. From the diversification-scale patterns of habitat occupation, major phylogenetic clades (A-D), geographic distribution, and knowledge from captive-maintained Sinocyclocheilus populations, we hypothesize habitat to be the major determinant of microbiome diversity, with phylogeny playing a lesser role. For this, we subject environmental water samples and fecal samples (representative of gut-microbiome) from 24 Sinocyclocheilus species, both from the wild and after being in captivity for six months, to bacterial 16S rRNA gene profiling using Illumina sequencing. We see significant differences in the gut microbiota structure of Sinocyclocheilus, reflective of the three habitat types; gut microbiomes too, were influenced by host-related factors. There is no significant association between the gut microbiomes and host phylogeny. However, there is some microbiome related structure at clade level, with the most geographically distant clades (A and D) being the most distinct, and two geographically overlapping clades (B and C) being similar. Microbes inhabiting water were not a cause for significant differences in fish-gut microbiota, but water quality parameters was. Transferring from wild to captivity, the fish microbiomes changed significantly and became homogenized, signifying adaptability and highlighting the importance of environmental factors (habitat) in microbiome community assembly. The core microbiome of this group closely resembled that of other teleost fishes. Our results suggest that divergent selection giving rise to evolutionary novelties also includes the microbiome of these fishes, which provides a functional advantage for life in the resource-depleted cave environment. SIGNIFICANCE STATEMENTThe largest diversification of cavefishes of the world, Sinocyclocheilus, not only show that habitat, and phylogenetic clade is important in determining their gut microbiome, but also that they reach a common microbiome in captivity irrespective of their phylogenetic position, region of origin and habitat, indicating that they are adaptable in the context of microbe related changes in their environment.

microbiology↗

bioRxiv2021

CyanoHABs: inevitable evolutionary ecological consequence for low nutrient-requiring cyanobacteria in water eutrophication

Cyanobacterial harmful algal blooms (CyanoHABs) arise as cyanobacteria dominate phytoplankton communities when nutrient levels increase from oligotrophic state. From a wholistic perspective, this longstanding altered phytoplankton structure results from two conditions: one sufficient condition that cyanobacteria can grow maximally with elevated nutrients; one necessary condition that co-living algae cannot grow fast or dominate at the same levels. The sufficient condition, the special mechanism of CyanoHABs at the population level, has been established as the synergistic interaction between superior cyanobacterial ecophysiology and elevated nutrients. But it is unknown how these functions arise or whether they are under directed evolution to water eutrophication. The necessary condition, the general mechanism of CyanoHABs at the community level, is little understood: why co-living algae cannot form blooms as cyanobacteria? Literature and bioinformatics analyses show that the superior ecophysiology undergoes no directed positive evolution to worldwide eutrophication in general or any local eutrophic waters in particular; instead, these functions are under strong purifying selection and likely acquired through early adaptive radiation in nutrient-deficient conditions, as functions enabling extant cyanobacteria to occupy other niches. The general mechanism turns out to be quite straightforward: cyanobacteria are simple life forms and thus have lower per capita nutrient demand for growth, compared to co-existing eukaryotic algae in cell size and structure, genome size, size of genome-scale metabolic networks, cell content, nutrient requirement. Lower nutrient demand is proved by existing field nutrient supplementation. Both the special and general mechanisms of CyanoHABs are tentative frameworks awaiting further theoretic improvement and empirical assessment.

evolutionary biology↗

bioRxiv2021

Microbial ecology of sulfur biogeochemical cycling at a mesothermic hot spring atop Northern Himalayas, India

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=146 SRC="FIGDIR/small/470874v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@1dfd0d5org.highwire.dtl.DTLVardef@107811forg.highwire.dtl.DTLVardef@1ae4af6org.highwire.dtl.DTLVardef@1bb90a1_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG Sulfur Related Prokaryotes (SRP) residing in hot spring present good opportunity for exploring the limitless possibilities of integral ecosystem processes. Metagenomic analysis further expand the phylogenetic breadth of these extraordinary sulfur metabolizing microorganisms, as well a their complex metabolic networks and syntrophic interactions in environmental biosystems. Through this study, we explored and expanded the microbial genetic repertoire with focus on sulfur cycling genes through metagenomic analysis of sulfur (S) contaminated hot spring, located at the Northern Himalayas. The analysis revealed rich diversity of microbial consortia with established roles in S cycling such as Pseudomonas, Thioalkalivibrio, Desulfovibrio and Desulfobulbaceae (Proteobacteria). The major gene families inferred to be abundant across microbial mat, sediment and water were assigned to Proteobacteria as reflected from the RPKs (reads per kilobase) categorized into translation and ribosomal structure and biogenesis. Analysis of sequence similarity showed conserved pattern of both dsrAB genes (n=178) retrieved from all metagenomes while other sulfur disproportionation proteins were diverged due to different structural and chemical substrates. The diversity of sulfur oxidizing bacteria (SOB) and sulfate reducing bacteria (SRB) with conserved (r)dsrAB suggests for it to be an important adaptation for microbial fitness at this site. Here, we confirm that (i) SRBs belongs to{delta} -Proteobacteria occurring independent LGT of dsr genes to different and few novel lineages (ii) also, the oxidative and reductive dsr evolutionary time scale phylogeny, proved that the earliest (not first) dsrAB proteins belong to anaerobic Thiobacillus with other (rdsr) oxidizers. Further, the structural prediction of unassigned DsrAB proteins confirmed their relatedness with species of Desulfovibrio (TM score= 0.86; 0.98; 0.96) and Archaeoglobus fulgidus (TM score= 0.97; 0.98). We proposed that the genetic repertoire might provide the basis of studying time scale evolution and horizontal gene transfer of these genes in biogeochemical S cycling and the complementary genes could be implemented in biotechnology and bioremediation applications.

microbiology↗

bioRxiv2021

Meta Analysis of the Ralstonia solanacearum species complex (RSSC) based on comparative evolutionary genomics and reverse ecology

Ralstonia solanacearum species complex (RSSC) strains are bacteria that colonize plant xylem and cause vascular wilt diseases. However, individual strains vary in host range, optimal disease temperatures, and physiological traits. To increase our understanding of the evolution, diversity, and biology of the RSSC, we performed a meta-analysis of 100 representative RSSC genomes. These 100 RSSC genomes contain 4,940 genes on average, and a pangenome analysis found that there are 3,262 genes in the core genome ([~]60% of the mean RSSC genome) with 13,128 genes in the extensive flexible genome. Although a core genome phylogenetic tree and a genome similarity matrix aligned with the previously named species (R. solanacearum, R. pseudosolanacearum, R. syzygii) and phylotypes (I-IV), these analyses also highlighted an unrecognized sub-clade of phylotype II. Additionally, we identified differences between phylotypes with respect to gene content and recombination rate, and we delineated population clusters based on the extent of horizontal gene transfer. Multiple analyses indicate that phylotype II is the most diverse phylotype, and it may thus represent the ancestral group of the RSSC. Additionally, we also used our genome-based framework to test whether the RSSC sequence variant (sequevar) taxonomy is a robust method to define within-species relationships of strains. The sequevar taxonomy is based on alignments of a single conserved gene (egl). Although sequevars in phylotype II describe monophyletic groups, the sequevar system breaks down in the highly recombinogenic phylotype I, which highlights the need for an improved cost-effective method for genotyping strains in phylotype I. Finally, we enabled quick and precise genome-based identification of newly sequenced Ralstonia strains by assigning Life Identification Numbers (LINs) to the 100 strains and by circumscribing the RSSC and its sub-groups in the LINbase Web service. IMPACT STATEMENTThe Ralstonia solanacearum species complex (RSSC) includes dozens of economically important pathogens of many cultivated and wild plants. The extensive genetic and phenotypic diversity that exists within the RSSC has made it challenging to subdivide this group into meaningful subgroups with relevance to plant disease control and plant biosecurity. This study provides a solid genome-based framework for improved classification and identification of the RSSC by analyzing one hundred representative RSSC genome sequences with a suite of comparative evolutionary genomic tools. The results also lay the foundation for additional in-depth studies to gain further insights into evolution and biology of this heterogeneous complex of destructive plant pathogens. DATA SUMMARYThe authors confirm that all raw data and code and protocols have been provided within the manuscript. All publicly available sequencing data used for analysis have been supplemented with accession numbers to access the data. The assembled genome of strain 19-3PR_UW348 was submitted to NCBI under Bioproject PRJNA775652 Biosample SAMN22612291. This Whole Genome Shotgun project has been deposited at GenBank under the accession JAJMMU000000000. The version described in this paper is version JAJMMU010000000.

genomics↗