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bioRxiv2018

On the timing of bill length evolution in British great tits: A comment on Bosse et al. 2017.

Long-term field studies coupled with quantitative genomics offer a powerful means to understand the genetic bases underlying quantitative traits and their evolutionary changes. However, analyzing and interpreting the time scales at which adaptive evolution occurs is challenging. First, while evolution is predictable in the short term, with strikingly rapid phenotypic changes in data series, it remains unpredictable in the long term. Second, while the temporal dynamics of some loci with large effect on phenotypic variation and fitness have been characterized, this task can be complicated in cases of highly polygenic trait architecture implicating numerous small effect size loci, or when statistical tests are sensitive to the heterogeneity of some key characteristics of the genome, like recombination rate variations. After introducing these aforementioned challenges, we discuss a recent investigation of the genomic architecture and spatio-temporal variation in great tit bill length, which was related to the recent use of bird feeders. We discuss how this case study illustrates the importance of considering different temporal scales and evolutionary mechanisms both while analyzing trait temporal trends and when searching for and interpreting the signals of putative genomic footprints of selection. More generally this commentary discusses interesting challenges for unraveling the time scale at which adaptive traits evolve and their genomic bases.\n\nImpact summaryAn important goal in evolutionary biology is to understand how individual traits evolve, leading to fascinating variations in time and space. Long-term field studies have been crucial in trying to understand the timing, extent, and ecological determinants of such trait variation in wild populations. In this context, recent genomic tools can be used to look for the genetic bases underlying such trait variation and can provide clues on the nature and timing of their evolution. However, the analysis and the interpretation of the time scales at which evolution occurs remain challenging. First, analyzing long-term data series can be tricky; short-term changes are highly predictable whereas long-term evolution is much less predictable. A second difficult task is to study the architecture of complex quantitative traits and to decipher the timing and roles of the several genomic mechanisms involved in their evolution. This commentary introduces these challenges and discusses a recent investigation of the nature and timing of ecological and genomic factors responsible for variation in great tit bill length. Overall, we raise cautionary warnings regarding several conceptual and technical features and limitations when coupling analyses of long-term and genomic data to study trait evolution in wild populations.

evolutionary biology↗

bioRxiv2018

Small differences in learning speed for different food qualities can drive efficient collective foraging in ant colonies

Social insects frequently make important collective decisions, such as selecting the best food sources. Many collective decisions are achieved via communication, for example by differential recruitment depending on resource quality. However, even species without recruitment can respond to a changing environment on collective level by tracking food source quality.\n\nWe hypothesised that an apparent collective decision to focus on the highest quality food source can be explained by differential learning of food qualities. Ants may learn the location of higher quality food faster, with most ants finally congregating at the best food source.\n\nTo test the effect of reward quality and motivation on learning in Lasius niger, we trained individual ants to find a reward of various sucrose molarities on one arm of a T-maze in spring and in autumn after one or four days of starvation.\n\nAs hypothesised, ants learned fastest in spring and lowest in autumn, with reduced starvation leading to slower learning. Surprisingly, the effect of food quality and motivation on the learning speed of individuals which persisted in visiting the feeders was small. However, persistence rates varied dramatically: All ants in spring made all (6) return visits to all food qualities, in contrast to 33% of ants in autumn under low starvation.\n\nFitting the empirical findings into an agent-based model revealed that even a tendency of ants to memorise routes to high quality food sources faster can result in ecologically sensible colony-level behaviour. Low motivation colonies are also choosier, due to increasing sensitivity to food quality.\n\nSignificance statementCollective decisions of insects are often achieved via communication and/or other interactions between individuals. However, animals can also make collective decisions in the absence of communication.\n\nWe show that foraging motivation and food quality can affect both route memory and the likelihood to return to the food source and thus mediate selective food exploitation. An agent-based model, implemented with our empirical findings, demonstrates that, at the collective level, even small differences in learning lead to ecologically sensible behaviour: mildly starved colonies are selective for high quality food while highly starved colonies exploit all food sources equally.\n\nWe therefore suggest that non-interactive factors such as individual learning and the foraging motivation of a colony can mediate or even drive group level behaviour. Instead of accounting collective behaviour exclusively to social interactions, possible contributing individual processes should also be considered.

animal behavior and cognition↗

bioRxiv2018

Finding Nemo’s Genes: A chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula

The iconic orange clownfish, Amphiprion percula, is a model organism for studying the ecology and evolution of reef fishes, including patterns of population connectivity, sex change, social organization, habitat selection and adaptation to climate change. Notably, the orange clownfish is the only reef fish for which a complete larval dispersal kernel has been established and was the first fish species for which it was demonstrated that anti-predator responses of reef fishes could be impaired by ocean acidification. Despite its importance, molecular resources for this species remain scarce and until now it lacked a reference genome assembly. Here we present a de novo chromosome-scale assembly of the genome of the orange clownfish Amphiprion percula. We utilized single-molecule real-time sequencing technology from Pacific Biosciences to produce an initial polished assembly comprised of 1,414 contigs, with a contig N50 length of 1.86 Mb. Using Hi-C based chromatin contact maps, 98% of the genome assembly were placed into 24 chromosomes, resulting in a final assembly of 908.8 Mb in length with contig and scaffold N50s of 3.12 and 38.4 Mb, respectively. This makes it one of the most contiguous and complete fish genome assemblies currently available. The genome was annotated with 26,597 protein coding genes and contains 96% of the core set of conserved actinopterygian orthologs. The availability of this reference genome assembly as a community resource will further strengthen the role of the orange clownfish as a model species for research on the ecology and evolution of reef fishes.

genomics↗

bioRxiv2018

Genetic dissection of assortative mating behavior

The evolution of new species is made easier when traits under divergent ecological selection are also mating cues. Such ecological mating cues are now considered more common than previously thought, but we still know little about the genetic changes underlying their evolution, or more generally about the genetic basis for assortative mating behaviors. The warning patterns of Heliconius melpomene and H. cydno are under disruptive selection due to increased predation of non-mimetic hybrids, and are used during mate recognition. We carried out a genome-wide quantitative trait locus (QTL) analysis of preference behaviors between these species and showed that divergent male preference has a simple genetic basis. Three QTLs each explain a large proportion of the differences in preference behavior observed between the parental species. Two of these QTLs are on chromosomes with major color pattern genes, including one that is tightly associated with the gene optix. Different loci influence different aspects of attraction, suggesting that behavioral isolation in Heliconius involves the evolution of independently segregating modules, similar to those for the corresponding wing pattern cues. Hybridization and subsequent sharing of wing pattern loci has played an important role during adaptation and speciation in Heliconius butterflies. The existence of large effect preference loci could similarly assist the evolution of novel behavioral phenotypes through recombination and introgression, and should facilitate rapid speciation.

evolutionary biology↗

bioRxiv2018

Mechanisms for European Bat Lyssavirus subtype 1 persistence in non-synanthropic bats: insights from a modeling study

BackgroundLyssaviruses are pathogens of bat origin of considerable zoonotic concern being the causative agent for rabies disease, however our understanding of their persistence in bat populations remains very scarce.\n\nMethodsLeveraging existing data from an extensive ecological field survey characterizing Myotis myotis and Miniopterus schreibersii bat species in the Catalonia region, we develop a data-driven spatially explicit metapopulation model to identify the mechanisms of the empirically observed persistence of European Bat Lyssavirus subtype 1 (EBLV-1), the most common lyssavirus species found in Europe. We consider different disease progressions accounting for lethal infection, immunity waning, and potential cross-species transmission when the two populations share the same refuge along the migratory path of M. schreibersii.\n\nResultsWe find that EBLV-1 persistence relies on host spatial structure through the migratory nature of M. schreibersii bats, on cross-species mixing with M. myotis population, and on a disease progression leading to survival of infected animals followed by temporary immunity. The higher fragmentation along the northern portion of the migratory path is necessary to maintain EBLV-1 sustained circulation in both species, whereas persistence would not be ensured in the single colony of M. myotis. Our study provides first estimates for the EBLV-1 transmission potential in M. schreibersii bats and average duration of immunity in the host species, yielding values compatible with previous empirical observations in M. myotis bats.\n\nConclusionsHabitats sharing and the strong spatial component of EBLV-1 transmission dynamics identified as key drivers in this ecological context may help understanding the observed spatial diffusion of the virus at a larger scale and across a diverse range of host species, through long-range migration and seeding of local populations. Our approach can be readily adapted to other zoonotic pathogens of public health concern.

epidemiology↗

bioRxiv2018

Metabolic modeling of Pectobacterium parmentieri SCC3193 provides insights into metabolic pathways of plant pathogenic bacteria

Understanding the plant-microbe interactions are crucial for improving plant productivity and plant protection. The latter aspect is particularly relevant for sustainable agriculture and development of new preventive strategies against the spread of plant diseases. Constraint-based metabolic modeling is providing one of the possible ways to investigate the adaptation to different ecological niches and may give insights into the metabolic versatility of plant pathogenic bacteria. In this study, we present a curated metabolic model of the emerging plant pathogenic bacterium Pectobacterium parmentieri SCC3193. Using flux balance analysis (FBA), we predict the metabolic adaptation to two different ecological niches, relevant for the persistence and the plant colonization by this bacterium: soil and rhizosphere. We performed in silico gene deletions to predict the set of core essential genes for this bacterium to grow in such environments. We anticipate that our metabolic model will be a valuable element for defining a set of metabolic targets to control infection and spreading of this plant pathogen and a scaffold to interpret future -omics datasets for this bacterium.

systems biology↗

bioRxiv2018

DNA metabarcoding from sample fixative as a quick and voucher preserving biodiversity assessment method

Metabarcoding is a powerful tool for biodiversity assessment and has become increasingly popular in recent years. Although its reliability and applicability have been proven in numerous scientific studies, metabarcoding still suffers from some drawbacks. One is the usually mandatory destruction of specimens before DNA extraction, which is problematic because it does not allow a later taxonomic evaluation of the results. Additionally, metabarcoding often implements a time-consuming step, where specimens need to be separated from substrate or sorted in different size classes. A non-destructive protocol, excluding any sorting step, where the extraction of DNA is conducted from a samples fixative (ethanol) could serve as an alternative. We test an innovative protocol, where the sample preserving ethanol is filtered and DNA extracted from the filter for subsequent DNA metabarcoding. We first tested the general functionality of this approach on 15 mock communities comprising one individual of eight different macroinvertebrate taxa each and tried to increase DNA yield through different treatments (ultrasonic irradiation, shaking, freezing). Application of the method was successful for most of the samples and taxa, but showed weaknesses in detecting mollusc taxa. In a second step, the community composition detected in DNA from ethanol was compared to conventional bulk sample metabarcoding of complex environmental samples. We found that especially taxa with pronounced exoskeleton or shells (Coleoptera, Isopoda) and small taxa (Trombidiformes) were underrepresented in ethanol samples regarding taxa diversity and read numbers. However, read numbers of Diptera (mainly chironomids) and Haplotaxida were higher in ethanol derived DNA samples, which might indicate the detection of stomach content, which would be an additional advantage of this approach. Concerning EPT (Ephemeroptera, Plecoptera, Trichoptera) taxa which are decisive for the determination of ecological statuses, both methods had 46 OTUs in common with 4 unique to the ethanol samples and 10 to the bulk samples. Results indicate that fixative-based metabarcoding is a non-destructive, time-saving alternative for biodiversity assessments focussing on taxa used for ecological status determination. For a comprehensive picture on total biodiversity, the method might however not be sufficient and conventional bulk sample metabarcoding should be applied.

molecular biology↗

bioRxiv2018

Intraspecific genetic and phenotypic diversity: parallel processes and correlated patterns?

Intraspecific diversity plays a key role for evolutionary and ecological dynamics. It is the raw material on which acts selection, it improves species and communities resilience to disturbance and it affects the way species modulate their biotic and abiotic environment. Understanding patterns and underlying determinants of genetic and phenotypic intraspecific diversity is therefore of critical importance for ecological, evolutionary and conservation sciences. Here, focusing on two freshwater fish species (Gobio occitaniae and Phoxinus phoxinus) sampled across a large river basin (the Garonne-Dordogne river basin, France), we used causal analyses to test for genetic-phenotypic intraspecific diversity correlations (GPIDCs) and unravel the processes underlying intraspecific diversity patterns. Genetic diversity was assessed using microsatellite markers and phenotypic diversity was assessed through geometric morphometrics. We found disparities in the distribution of genetic and phenotypic diversity in the two species, suggesting higher level of local adaptation in G. occitaniae, and our results revealed common and contrasted processes shaping diversity at the - and {beta}-level. At the -level, we found no GPIDC in both species despite common relations between isolation and genetic and phenotypic -diversity in G. occitaniae. At the {beta}-level, we found no GPIDC in P. phoxinus but we found a positive GPIDC in G. occitaniae. This correlation appeared to be caused by a direct impact of one facet of intraspecific diversity on the other, and we speculated that it could originate from positive assortative mating. Studying neutral genetic diversity and phenotypic diversity within an integrative framework appears as a valuable way of deciphering the complex and diverse impacts of neutral and adaptive processes on intraspecific diversity patterns.

evolutionary biology↗

bioRxiv2018

Sexual reproduction in the fungal foliar pathogen Zymoseptoria tritici is driven by antagonistic density-dependence mechanisms

This study provides empirical evidence for antagonistic density-dependence mechanisms driving sexual reproduction in the wheat fungal pathogen Zymoseptoria tritici. Biparental crosses with 12 increasing inoculum concentrations, in controlled conditions, showed that sexual reproduction in Z. tritici was impacted by an Allee effect due to mate limitation and a competition with asexual multiplication for resource allocation. We found that asexual multiplication was itself affected by competition for host resources between the two parental isolates, as illustrated by the decrease in asexual fruiting body density and sporulation intensity observed with increasing lesion density. Consistent with these results for controlled co-inoculation, we found that the intensity of sexual reproduction varied with both cropping period and the vertical position of the host tissues in the field. An optimal lesion density maximizing offspring (ascospores) number was established, and its eco-evolutionary consequences are considered here. Two ecological mechanisms may be involved: competition for resources between the two modes of reproduction (decrease in the host resources available for sexual reproduction due to their prior use in asexual multiplication), and competitive disequilibrium between the two parental isolates, due to differential interaction dynamics with the host, for example, leading to an imbalance between mating types. Conceptual models based on these results suggest that sexual reproduction plays a key role in the evolution of pathogenicity traits, including virulence and aggressiveness. Ecological knowledge about the determinants of sexual reproduction in Z. tritici may, therefore, open up new perspectives for the management of other fungal foliar pathogens with dual modes of reproduction.

microbiology↗

bioRxiv2018

A single loss of photosynthesis in diatoms

Loss of photosynthesis is a common and often repeated trajectory in nearly all major groups of photosynthetic eukaryotes. One small subset of apochloritic diatoms in the genus Nitzschia have lost their ability to photosynthesize and require extracellular carbon for growth. Similar to other secondarily nonphotosynthetic taxa, apochloritic diatoms maintain colorless plastids with highly reduced plastid genomes. Although the narrow taxonomic breadth of apochloritic diatoms suggests a single loss of photosynthesis in the common ancestor of these species, previous phylogenetic analyses suggested that photosynthesis was lost multiple times. We sequenced additional phylogenetic markers from the nuclear and mitochondrial genomes for a larger set of taxa and found that the best trees for datasets representing all three genetic compartments provided low to moderate support for monophyly of apochloritic Nitzschia, consistent with a single loss of photosynthesis in diatoms. We sequenced the plastid genome of one apochloritic species and found that it was highly similar in all respects to the plastid genome of another apochloritic Nitzschia species, indicating that streamlining of the plastid genome had completed prior to the split of these two species. Finally, it is increasingly clear that some locales host relatively large numbers apochloritic Nitzschia species that span the phylogenetic diversity of the group, indicating that these species co-exist because of resource abundance or resource partitioning in ecologically favorable habitats. A better understanding of the phylogeny and ecology of this group, together with emerging genomic resources, will help identify the factors that have driven and maintained the loss of photosynthesis in this group, a rare event in diatoms.

evolutionary biology↗

bioRxiv2018

Strength in numbers: collaborative science for new experimental model systems

Our current understanding of biology is heavily based on the contributions from a small number of genetically tractable model organisms. Most eukaryotic phyla lack such experimental models, and this limits our ability to explore the molecular mechanisms that ultimately define their biology, ecology, and diversity. In particular, marine protists suffer from a paucity of model organisms despite playing critical roles in global nutrient cycles, food webs, and climate. To address this deficit, an initiative was launched in 2015 to foster development of ecologically and taxonomically diverse marine protist genetic models. This multifaceted, complex but important challenge required a highly collaborative community-based approach. Herein we describe this approach, the advances achieved, and the lessons learned by participants in this novel community-based model for research.

microbiology↗

bioRxiv2018

Convergent transcriptomic landscapes under polygenic selection accompany inter-continental parallel evolution within a Nearctic Coregonus (Salmonidae) sister-species complex.

In contrast to the plethora of studies focusing on the genomic basis of adaptive phenotypic divergence, the role of gene expression during speciation has been much less investigated and consequently, less understood. Yet, the convergence of differential gene expression patterns between closely related species-pairs might reflect the role of natural selection during the process of ecological speciation. Here, we test for intercontinental convergence in differential transcriptional signatures between limnetic and benthic sympatric species-pairs of Lake Whitefish (Coregonus clupeaformis) and its sister-lineage, the European Whitefish (C. lavaretus), using six replicated sympatric species-pairs (two in North America, two in Norway and two in Switzerland). We characterized both sequence variation in transcribed regions and differential gene expression between sympatric limnetic and benthic species across regions and continents. Our first finding was that differentially expressed genes (DEG) between limnetic and benthic whitefish tend to be enriched in shared polymorphism among sister-lineages. We then used both genotypes and co-variation in expression in order to infer polygenic selection at the gene level. We identified parallel outliers and DEG involving genes primarily over-expressed in limnetic species relative to the benthic species. Our analysis finally revealed the existence of shared genomic bases underlying parallel differential expression across replicated species pairs from both continents, such as a cis-eQTL affecting the pyruvate kinase expression level involved in glycolysis. Our results are consistent with a longstanding role of natural selection in maintaining transcontinental diversity at phenotypic traits involved in ecological speciation between limnetic and benthic whitefishes.

evolutionary biology↗

bioRxiv2018

Rapid, inexpensive measurement of synthetic bacterial community composition by Sanger sequencing

Simple synthetic bacterial communities are powerful tools for studying microbial ecology and evolution, as they enable rapid iteration between controlled laboratory experiments and theoretical modeling. However, their utility is hampered by the lack of fast, inexpensive, and accurate methods for quantifying bacterial community composition. For instance, while next-generation amplicon sequencing can be very accurate, high costs (>$30 per sample) and turnaround times (>1 month) limit the nature and pace of experiments. Here, we introduce a new approach for quantifying composition in synthetic bacterial communities based on Sanger sequencing. First, for a given community, we PCR-amplify a universal marker gene (here, the 16S rRNA gene), which yields a mixture of amplicons. Second, we sequence this amplicon mixture in a single Sanger sequencing reaction, which produces a \"mixed\" electropherogram with contributions from each community member. We also sequence each community members marker gene individually to generate \"individual\" electropherograms. Third, we fit the mixed electropherogram as a linear combination of time-warped individual electropherograms, thereby allowing us to estimate the fractional amplicon abundance of each strain within the community. Importantly, our approach accounts for retention-time variability in electrophoretic signals, which is crucial for accurate compositional estimates. Using synthetic communities of marine bacterial isolates, we show that this approach yields accurate and reproducible abundance estimates for two-, four-, and seven-strain bacterial communities. Furthermore, this approach can provide results within one day and costs ~$5 USD per sample. We envision this approach will enable new insights in microbial ecology by increasing the number of samples that can be analyzed and enabling faster iteration between experiments and theory. We have implemented our method in a free and open-source R package called CASEU (\"Compositional Analysis by Sanger Electropherogram Unmixing\"), available at https://bitbucket.org/DattaManoshi/caseu.

bioinformatics↗

bioRxiv2018

Evolutionary emergence of infectious diseases in heterogeneous host populations

Emergence and re-emergence of pathogens are notoriously difficult to predict. The erratic nature of those events is reinforced by the stochastic nature of pathogen evolution during the early phase of an epidemic. For instance, mutations allowing pathogens to escape host resistance may boost pathogen spread and promote emergence. Yet, the ecological factors that govern such evolutionary emergence remain elusive both because of the lack of ecological realism of current theoretical frameworks and the difficulty of experimentally testing their predictions. Here we develop a theoretical model to explore the effects of the heterogeneity of the host population on the probability of pathogen emergence, with or without pathogen evolution. We show that evolutionary emergence and the spread of escape mutations in the pathogen population is more likely to occur when the host population contains an intermediate proportion of resistant hosts. We also show that lower pathogen inoculum size and higher diversity of host resistance decrease the probability of evolutionary emergence. Crucially, we present experimental confirmations of these predictions using lytic bacteriophages infecting their bacterial hosts containing diverse CRISPR-Cas immune defenses. We discuss the implications of these results for cross-species spillover and for the management of emerging infectious diseases.\n\nSignificance statementCan we predict the emergence of infectious diseases? The probability that an epidemic breaks out is highly dependent on the ability of the pathogen to acquire new adaptive mutations and to induce evolutionary emergence. Forecasting pathogen emergence thus requires a good understanding of the interplay between epidemiology and evolution taking place at the onset of an outbreak. Here, we provide a comprehensive theoretical framework to analyze the impact of host population heterogeneity on the probability of pathogen evolutionary emergence. We use this model to predict the impact of the fraction of susceptible hosts, the inoculum size of the pathogen and the diversity of host resistance on pathogen emergence. Our experiments using lytic bacteriophages and CRISPR-resistant bacteria support our theoretical predictions.

evolutionary biology↗

bioRxiv2018

Infections patterns and fitness effects of Rickettsia and Sodalis symbionts in the green lacewing Chrysoperla carnea

Endosymbionts are wide-spread among insects and can play an essential role in host ecology. The common green lacewing (Chrysoperla carnea s. str.) is a neuropteran insect species which is widely used as a biological pest control. We screened for endosymbionts in natural and laboratory populations of the green lacewing using diagnostic PCR amplicons. We found the endosymbiont Rickettsia to be very common in all screened populations, whereas a so far uncharacterized Sodalis strain was solely found in laboratory populations. The new Sodalis strain was characterized using a whole genome shotgun approach. Its draft genome revealed an approximate genome size of 4.3 Mbp and the presence of 5213 coding sequences. Phylogenomic analyses indicated that this bacterium is the sister taxon of S. praecaptivus. In an experimental approach, we found a negative impact of Sodalis on the reproduction success of the green lacewing. Co-infections with Rickettsia and Sodalis caused an even higher decrease of reproductive success than single Sodalis infections. In contrast, no significant fitness differences were found in Rickettsia infected green lacewings compared to uninfected lacewings. The Rickettsia/Sodalis/Ch. carnea system presents a promising model to study evolutionary endosymbiont-host interactions in Neuroptera and endosymbiont-endosymbiont interactions in general. The economic and ecological importance of green lacewings in biological pest control warrants a more profound understanding of its biology, which might be strongly influenced by symbionts.

evolutionary biology↗

bioRxiv2018

Effect of eco-remediation and microbial community using multilayer solar planted floating island (MS-PFI) in the drainage channel

A multilayer solar planted floating island (MS-PFI) planted with Eichhornia crassipes are potential alternatives to traditional PFI. The highest removal rates of suspended solids, total nitrogen, total phosphorus, ammonia nitrogen and chemical oxygen demand was 86%, 75%, 80%, 95% and 84%, respectively. Proteobacteria (average 43.4% of total sequences) and Actinobacteria (19.9%) were the dominant phyla. Numerous genus had obvious differences between influent and effluent water, for instance, 13, 12 and 7 % in effluent water were assigned to the hgcl_clade, Norank_c_Cyanobacteria, and Rhizorhapis, while their relative abundances were decreased to 5, 3 and 0 %. In contrast, a distinct increase among Flavobacterium (10%), Limnohabitans (7%), Alpinimonas (4%), norank_p_Saccharibacteria (4%), Erwinia (3%) after MS-PFI treatment. MS-PFI brings various bacteria involved in contaminant degradation and nutrient removal in biological wastewater treatment systems. An amount of {yen} 1,843 was totally inputted to construct floating bed, which was rarely needed operation and maintenance costs.\n\nImportanceIn-situ micro-polluted water ecological remediation, microorganisms and plants are effective to improve environmental quality and provide essential ecosystem services. Recently, we invent a new multilayer solar with an excellent pollutant removal efficiency. Microbes can decompose or mineralize organic matter effectively, also provide food for aquatic animals and increase nutrients or substances for plants, it is an important part of biogeochemical cycles and energy flows in aquatic ecological systems. However, few study explain the bacteria diversity and its responses between influent and effluent water in a planted floating island. The significance of our study is in identifying-in greater detail-the responses of bacteria in the new MS-PFI. This will greatly enhance our knowledge of bacteria communities, and can be widely used in micro-polluted water remediation.

bioengineering↗

bioRxiv2018

Stepping into a dangerous quagmire: environmental determinants of human-lancehead pit vipers (Bothrops genus) contact resulting in injuries, Brazilian Amazon

Despite significant and successful efforts in Brazil regarding snakebites in the areas of research, antivenom manufacture and quality control, training of health professionals in the diagnosis and clinical management of bites, little is known about determinants of snakebites incidence in order to further plan interventions to reduce the impact of this medical condition. Understanding the complexity of ecological interactions in a geographical region is important for prediction, prevention and control measures of snakebites. The aim of this investigation is to describe spatial distribution and identify environmental determinants of human- lancehead pit vipers (Bothrops genus) contact resulting in injuries, in the Brazilian Amazon. Aggregated data by municipality was used to analyze the spatial distribution of Bothrops bites cases and its relationship with geographic and environmental factors. Eight geo-environmental factors were included in the analysis as independent variables: (1) tree canopy loss increase; (2) area with vegetation cover; (3) area covered by water bodies; (4) altitude; (5) precipitation; (6) air relative humidity; (7) soil moisture; and (8) air temperature. Human- lancehead pit vipers (Bothrops genus) contact resulting in envenomings in the Amazon region is more incident in lowlands [-0.0006827 (IC95%: -0.0007705; - 0.0005949), p<0.0001], with high preserved original vegetation cover [0.0065439 (IC95%: 0.0070757; 0.0060121), p<0.0001], with heaviest rainfall [0.0000976 (IC95%: 0.0000925; 0.0001026), p<0.0001] and higher air relative humidity [- 0.0081773 (IC95%: -0.0107681; -0.0055865), p<0.0001]. This association is interpreted as the result of the higher forest productivity and abundance of pit vipers in such landscapes.\n\nAuthor summaryDespite successful efforts in Brazil regarding snakebites in the areas of research, antivenom manufacture and quality control and training of health professionals, little is known about determinants of snakebites incidence in order to further plan interventions to reduce the impact of this medical condition. Understanding the complexity of ecological interactions in a geographical region is important for prediction, prevention and control measures of snakebites. The aim of this study is to describe spatial distribution and identify environmental determinants of human- lancehead pit vipers (Bothrops genus) contact resulting in injuries, in the Brazilian Amazon. An increase in the forest productivity with a higher availability of some types of prey, such as frogs and amphibians, anurans and lizards, was suggested as a cause for the higher snake abundance in the rainy season. Probably due to the higher forest productivity and abundance of pit vipers in such landscapes, human-lancehead pit vipers contact resulting in envenomings in the Amazon region is more incident in lowlands, with high preserved original vegetation cover, with heaviest rainfall and higher air relative humidity.

animal behavior and cognition↗

bioRxiv2018

Available energy fluxes drive a phase transition in the diversity, stability, and functional structure of microbial communities

A fundamental goal of microbial ecology is to understand what determines the diversity, stability, and structure of microbial ecosystems. The microbial context poses special conceptual challenges because of the strong mutual influences between the microbes and their chemical environment through the consumption and production of metabolites. By analyzing a generalized consumer resource model that explicitly includes cross-feeding, stochastic colonization, and thermodynamics, we show that complex microbial communities generically exhibit a transition as a function of available energy fluxes from a "resource-limited" regime where community structure and stability is shaped by energetic and metabolic considerations to a diverse regime where the dominant force shaping microbial communities is the overlap between species consumption preferences. These two regimes have distinct species abundance patterns, different functional profiles, and respond differently to environmental perturbations. Our model reproduces large-scale ecological patterns observed across multiple experimental settings such as nestedness and differential beta diversity patterns along energy gradients. We discuss the experimental implications of our results and possible connections with disorder-induced phase transitions in statistical physics.

biophysics↗