Biology subjects

Nesme, J.

Publications and source records attributed to Nesme, J..

18 recordsLinked to original sources

bioRxiv2026

Convergent molecular changes in populations of two pipefish species in the Baltic Sea

While studies of molecular convergence typically focus on species that independently evolved similar phenotypes, similar questions can be asked among populations of different species adapting to the same environment. Here, we study the Baltic Sea environmental gradient and two co-distributed, ecologically similar, but distantly related pipefish species, the broadnosed pipefish (Syngnathus typhle) and the straightnose pipefish (Nerophis ophidion), to test whether independent colonization of the Baltic Sea led to similar population structure and caused convergence at different genomic levels. Using a new diploid genome for S. typhle and whole-genome resequencing data (N=99 for S. typhle; N=81 for N. ophidion) across seven locations from France to Finland, we identified stronger population structure in S. typhle than in N. ophidion, while both species showed differentiation between North Atlantic, Danish Straits, and Baltic Sea populations. Genetic diversity was lower in Baltic populations, particularly in S. typhle. Cross-species comparisons of Baltic populations revealed contrasting chromosome-level patterns of genomic differentiation, with differentiation spread across the genome in S. typhle but concentrated in specific chromosomal regions in N. ophidion. Nonetheless, we identified multiple orthologous genes and SNPs showing convergent differentiation in the Baltic populations of both species, including genes related to metabolism, immunity, and regulatory functions. Overall, we identified molecular convergence at the gene and nucleotide level between Baltic populations of distantly related pipefish species, while convergence was limited at broader genomic scales. These findings suggest that similar environmental pressures can repeatedly target specific genetic elements even when genomic backgrounds and population structures differ.

evolutionary biology↗

bioRxiv2026

Sea stickleback genome reveals repeated chromosomal rearrangements in sticklebacks

Sticklebacks (Gasterosteidae) encompass model organisms which are of particular interest for evolutionary and ecological genomics. Within Gasterosteidae, chromosome number is variable (2n=40-46) and independent fusions of homologous chromosomes have been proposed. The sea stickleback (or fifteen-spined stickleback, Spinachia spinachia ) has the lowest known number of chromosomes (2n=40) and hence is crucial in understanding chromosome evolution among sticklebacks, but is so far missing in genomic datasets. Here, we present a high-quality diploid genome assembly of S. spinachia. PacBio HiFi and Hi-C reads were assembled into a genome of 407.5 Mb in size, consisting of 20 chromosomes, with an N50 of 6.6 Mb and 98.96% complete single-copy BUSCO genes. A phylogenetic tree inferred across five stickleback species and four outgroup genomes from 19,156 genes, alongside synteny analyses and ancestral chromosome reconstructions, confirms S. spinachia as the sister species to the four-spined stickleback (Apeltes quadracus) and not as the sister group to all other sticklebacks as once thought. It has one species-specific chromosome fusion and shares two fusions with the three-spined stickleback (Gasterosteus aculeatus), none of which are present in its sister species. One of these fusions is also present in Pungitius, leading to reinterpretion of this fusion as ancestral to Gasterosteidae, with subsequent fission in Apeltes. This implies a lower ancestral chromosome number in Gasterosteidae (2n=44) than previously thought. The other fusion shared with G. aculeatus presents a case of convergence. Our results suggest that karyotype evolution in Gasterosteidae has been shaped by ancestral chromosome fusion, convergent fusion, and secondary fission.

evolutionary biology↗

bioRxiv2026

Multi-omics reveals mechanisms behind pathogen inhibition by a microalgal microbiome

Aquaculture is an essential food production sector for meeting the global demand for high-quality protein. However, the sector faces significant challenges from bacterial pathogens, particularly Vibrio anguillarum, which causes vibriosis in numerous commercially important fish species. Current disease management strategies rely heavily on antibiotics, leading to antimicrobial resistance and environmental concerns. Microalgal microbiomes represent promising alternatives for sustainable pathogen control, yet the molecular mechanisms underlying their inhibitory activity remain poorly understood. Here, we employed an integrated multi-omics approach to elucidate the mechanisms by which the microbiome of microalga Isochrysis galbana inhibits the highly virulent fish pathogen V. anguillarum strain 90-11-286. Using a GFP-based inhibition assay, we confirmed potent pathogen suppression by the algal microbiome, achieving complete inhibition at a 1:1000 ratio of pathogen to microbiome. Through 16S rRNA gene amplicon sequencing, metagenomics, metatranscriptomics, and metabolomics, we characterized community composition, genomic potential, gene expression patterns, and metabolite production during pathogen challenge. The inhibitory microbiome was dominated by Alteromonas macleodii and Vreelandella alkaliphila, with high-quality metagenome-assembled genomes revealing substantial secondary metabolite biosynthetic potential. Metatranscriptomic analysis revealed active expression of biosynthetic gene clusters encoding, for example, non-ribosomal peptide synthetases, particularly a siderophore gene cluster in V. alkaliphila. Metabolomic profiling confirmed the production of hydroxamate siderophores in the microbiome, including desferrioxamine analogues, proferrioxamine G1t, and tenacibactin D, which accumulated during pathogen inhibition, as well as 10 putative new compounds. Notably, siderophore production was constitutive rather than pathogen-induced, suggesting iron competition as the primary inhibitory mechanism. Our findings demonstrate that iron sequestration through siderophore production represents a key strategy for pathogen suppression in marine microbial communities. This work provides molecular evidence for microbiome-mediated disease control and establishes a foundation for developing rationally designed multi-strain probiotic consortia for sustainable aquaculture applications, offering an environmentally friendly alternative to antibiotic-based pathogen management strategies.

microbiology↗

bioRxiv2026

Evolutionary history and genomic vulnerability of the extinct giant deer Megaloceros giganteus

The extinct giant deer (Megaloceros giganteus) was one of the most striking megafaunal species of the Late Quaternary, distinguished by its enormous palmated antlers reaching up to 3.5 m across, the largest known among both living and extinct cervids. Despite its iconic status, little is known about its genomic history prior to extinction [~]8 thousand years ago (kya). We generated the first nuclear palaeogenomes for Megaloceros, represented by nine individuals from Germany ([~]40 kya) and Ireland ([~]11 kya), mapped to a new chromosome-level reference genome of the fallow deer (Dama dama). Phylogenomic analyses placed Megaloceros as sister to Dama (divergence [~]3.5 Ma) and revealed evidence of gene flow with ancestral Cervus lineages. Population analyses identified clear differentiation between German and Irish lineages, with higher genetic diversity in the German individuals. Two genes under strong positive selection, BNIPL and SLC10A7, are associated with apoptosis regulation and skeletal development/bone mineralisation, respectively, and may relate to the species large body and antler size. Demographic reconstructions indicate a long-term decline in effective population size, extremely low heterozygosity, little evidence of extensive runs of homozygosity, and an elevated burden of predicted deleterious alleles. Together, these results suggest that Megaloceros entered the terminal Pleistocene in a genomically fragile state, offering new insight into the biology and evolutionary legacy of one of the largest and most distinctive cervids that ever lived.

evolutionary biology↗

bioRxiv2025

Convergent Evolution of Sociality Causes Reduction of Mutation Rates in Spiders

Germline mutation rates influence the pace of molecular evolution, yet the roles of selection and life history in shaping their evolution remain to be determined. Comparative systems with replicated evolutionary transitions provide a unique opportunity to determine how changes in life history influence germline mutation rates. In the spider genus Stegodyphus, permanent sociality evolved independently three times within the past million years and is associated with obligate inbreeding, female-biased sex ratios, reduced fecundity, and sharply reduced effective population sizes. We sequenced 202 parent-offspring trios from 34 full-sibling families across three social and four closely related subsocial species and analysed quality-filtered trios in a phylogenetic comparative framework. Each independent transition to sociality was associated with an approximately 2-fold reduction in the de novo mutation rate in the germline. Phylogenetic analyses of synonymous branch lengths suggest that the mutation rates declined in parallel with the transitions to sociality. These rapid reductions in mutation rates in social lineages with small effective population sizes run counter to the drift-barrier hypothesis, which predicts that reduced selection efficacy would lead to higher mutation rates. We find no evidence that reduced mutation rates in the social species was favoured by selection for improving DNA repair efficiency, since there is no upregulation of DNA repair pathway genes in the ovaries of the social species. On the contrary, the mutation rate is reduced across mutational classes and in somatic tissue in social species compared with their subsocial counterparts. These patterns suggest that the reduction in mutation rate in social spiders is a consequence of convergent life history changes, including reduced body size and production of fewer, larger eggs. Our results highlight that the evolution of sociality, which entails major life history changes, can rapidly reshape fundamental evolutionary parameters, such as the germline mutation rate.

evolutionary biology↗

bioRxiv2025

Climate change impacts the structure and nitrogen-fixing activities of subarctic feather moss microbiomes across a precipitation gradient

Associations between feather mosses and cyanobacteria are crucial sources of new biologically available nitrogen (N) in arctic and subarctic ecosystems. The physiology of both mosses and cyanobacteria is strongly influenced by environmental factors such as temperature and moisture, which directly affect N2 fixation rates. These associations may be threatened by climate change, since it leads to warmer and drier conditions in polar regions. In this study, we investigated the N2-fixing microbial communities associated with two common feather mosses across a precipitation gradient in the subarctic tundra, followed by a temperature and moisture experiment. Using acetylene reduction assays, nifH gene sequencing and qPCR, we evaluated how shifts in temperature and moisture influence nitrogenase activity and N2-fixing community structure. Our results showed that N2 fixation was highest in sites with greater precipitation and increased with both temperature and moisture. Cyanobacteria dominated N2-fixing communities, but currently unclassified bacteria also seemed to play a significant role, particularly at high temperatures. The number of cyanobacterial nifH copies tended to decrease with temperature, while the relative abundance of unclassified bacteria increased. These findings suggest that the N2-fixing activity, abundance and diversity of cyanobacteria associated with feather mosses in the subarctic will decline under warmer and drier conditions, potentially leading to a shift in the composition of feather moss-associated microbial communities in a warmer Arctic, with potential consequences for N input into the ecosystem.

ecology↗

bioRxiv2025

Accurate plasmid reconstruction from metagenomics data using assembly-alignment graphs and contrastive learning

Plasmids are extrachromosomal DNA molecules that enable horizontal gene transfer in bacteria, often conferring advantages such as antibiotic resistance. Despite their significance, plasmids are underrepresented in genomic databases due to challenges in assembling them, caused by mosaicism and micro-diversity. Current plasmid assemblers rely on detecting circular paths in single-sample assembly graphs, but face limitations due to graph fragmentation and entanglement, and low coverage. We introduce PlasMAAG (Plasmid and organism Metagenomic binning using Assembly Alignment Graphs), a framework to recover plasmids and organisms from metagenomic samples that leverages an approach that we call "assembly-alignment graphs" alongside common binning features. On synthetic benchmark datasets, PlasMAAG reconstructed 50-121% more near-complete plasmids than competing methods and improved the Matthews Correlation Coefficient of geNomad contig classification by 28-106%. On hospital sewage samples, PlasMAAG outperformed all other methods, reconstructing 33% more plasmid sequences. PlasMAAG enables the study of organism-plasmid associations and intra-plasmid diversity across samples, offering state-of-the-art plasmid reconstruction with reduced computational costs.

bioinformatics↗

bioRxiv2023

A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics

Shotgun metagenomics enables the reconstruction of complex microbial communities at a high level of detail. Such an approach can be conducted using both short-read and long-read sequencing data, as well as a combination of both. To assess the pros and cons of these different approaches, we used 22 faecal DNA extracts collected weekly for 11 weeks from two respective lab mice to study seven performance metrics over four combinations of sequencing depth and technology: i) 20 Gbp of Illumina short-read data, ii) 40 Gbp of short-read data, iii) 20 Gbp of PacBio HiFi long-read data, and iv) 40 Gbp of hybrid (20 Gbp of short-read + 20 Gbp of long-read) data. No strategy was best for all metrics, but instead, each one excelled across different metrics. The long-read approach yielded the best assembly statistics, with the highest N50 and lowest number of contigs. The 40 Gbp short-read approach yielded the highest number of refined bins. Finally, the hybrid approach yielded the longest assemblies, and the highest mapping rate to the bacterial genomes. Our results suggest that while long-read sequencing significantly improves the quality of reconstructed bacterial genomes, it is more expensive and requires deeper sequencing than short-read approaches to recover a comparable amount of reconstructed genomes. The most optimal strategy is study-specific, and depends on how researchers assess the tradeoff between the quantity and quality of recovered genomes. ImportanceOur understanding of microbial communities is limited by the technologies we employ. Here, we test several different DNA sequencing techniques to better understand the pros and cons of each. Long read DNA sequencing allowed for the reconstruction of higher quality and even complete microbial genomes, however, the cost was greater than commonly used short-read DNA sequencing. We suggest researchers consider the trade-offs between each method and decide based on the goals of their research question/s.

microbiology↗

bioRxiv2023

The role of plasmids in the gut microbiome during the first year of life

Plasmids are extrachromosomal self-replicating genetic elements that play a key role in bacterial ecology and evolution by shuttling diverse host-beneficial traits between bacteria. However, our understanding of plasmids is still limited, particularly in the human gut microbiota, and little is known about how they are acquired and become established in infants. In this study, we explored a longitudinal fecal metagenomic dataset obtained from 98 Swedish children who were followed during their first year of life. For this, we developed a bioinformatics pipeline for the complete sequence assembly and annotation of plasmids, together with the identification of plasmid contigs. We found that gut plasmids in these children were extremely diverse, particularly in the first four months of life, and this diversity decreased with maturation of the gut microbiota. Members of genera Bacteroides and Bifidobacterium were identified as major hosts of transmissible plasmids and important hubs of horizontal gene transfer in the early human gut microbiota. Additionally, we discovered that plasmids played a substantial role in expanding the gene repertoires of their bacterial hosts: approximately a quarter of unannotated plasmid genes were found only on plasmids and not on chromosomes. Together, our results provide the first characterization of the early acquisition and development of plasmids in the infant gut microbiome. Their diversity and abundance in the first months of life could benefit a variable and rapidly proliferating microbiota by providing increased adaptability in a highly competitive environment.

microbiology↗

bioRxiv2023

Co-localization of antibiotic resistance genes is widespread in the infant gut microbiome and associates with an immature gut microbial composition

Even in the absence of antibiotic exposure, the gut microbiome of infants has been shown to contain numerous antibiotic resistance genes (ARGs), but the mechanism for this remains unclear. In environmental bacteria, the selective advantage of ARGs can be increased through co-localization with genes such as other ARGs, biocide resistance genes, metal resistance genes, and virulence genes. However, this phenomenon is unknown from the human gut microbiome during early life despite frequent exposures to biocides and metals from an early age. Here, we conducted a comprehensive analysis of genetic co-localization of resistance genes in a cohort of 662 Danish children and examined the association between such co-localization and environmental factors as well as gut microbial maturation. Our study showed that co-localization of ARGs with other resistance and virulence genes is common in the early gut microbiome and is associated with gut bacteria that are indicative of low maturity, especially E. coli. The most common forms of co-localization involved tetracycline and fluoroquinolone resistance genes located near other ARGs, and, on plasmids, co-localization predominantly occurred in the form of class 1 integrons. Antibiotic use caused a short-term increase in mobile ARGs, while non-mobile ARGs showed no significant change. Finally, we found that a high abundance of virulence genes was associated with low gut microbial maturity and that virulence genes showed even higher potential for mobility than ARGs. Our study highlights important constraints that need to be considered when developing strategies to combat ARG dissemination.

microbiology↗

bioRxiv2022

Plasmid Permissiveness of Wastewater Microbiomes can be Predicted from 16S rDNA sequences by Machine Learning

Wastewater Treatment Plants (WWTPs) contain a diverse microbial community with high cell density. They constantly receive antimicrobial residues and resistant strains and, therefore, may offer conditions for the Horizontal Gene Transfer (HGT) of antimicrobial resistance determinants, transmitting clinically important genes between, e.g., enteric and environmental bacteria and vice versa. Despite the clinical importance, tools for predicting HGT are still under-developed. In this study, we examined to which extent microbial community composition, as inferred by partial 16S rRNA gene sequences, can predict plasmid permissiveness, i.e., the ability of cells to receive a plasmid through conjugation, for microbial communities in the water cycle, using data from standardized filter mating assays using fluorescent bio-reporter plasmids. We leveraged a range of machine learning models for predicting the permissiveness for each taxon in the community, translating to the range of hosts a plasmid is able to transfer to, for three broad host-range resistance plasmids (pKJK5, pB10, and RP4). Our results indicate that the predicted permissiveness from the best performing model (random forest) showed a moderate-to-strong average correlation of 0.45 for pB10 (95% CI: 0.42-0.52), 0.42 for pKJK5 (0.95% CI: 0.38-0.45) and 0.52 for RP4 (0.95% CI:0.45-0.55) with the experimental permissiveness in the unseen test dataset. Predictive phylogenetic signals occurred despite these being broad host-range plasmids. Our results provide a framework that contributes to assessing the risk of AMR pollution in wastewater systems. The predictive tool is available as a an application under https://github.com/DaneshMoradigaravand/PlasmidPerm.

bioinformatics↗

bioRxiv2021

CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids

Many prokaryotes encode CRISPR-Cas systems as immune protection against mobile genetic elements (MGEs), yet, a number of MGEs also harbor CRISPR-Cas components. With a few exceptions, CRISPR-Cas loci encoded on MGEs are uncharted and a comprehensive analysis of their distribution, prevalence, diversity, and function is lacking. Here, we systematically investigated CRISPR-Cas loci across the largest curated collection of natural bacterial and archaeal plasmids. CRISPR-Cas loci are widely but heterogeneously distributed across plasmids and, in comparison to host chromosomes, their mean prevalence per Mbp is higher and their distribution is markedly distinct. Furthermore, the spacer content of plasmid CRISPRs exhibits a strong targeting bias towards other plasmids, while chromosomal arrays are enriched with virus-targeting spacers. These contrasting targeting preferences dominate across the diversity of CRISPR-Cas subtypes and host taxa, highlighting the genetic independence of plasmids and suggesting a major role of CRISPR-Cas for mediating plasmid-plasmid conflicts. Altogether, CRISPR-Cas are frequent accessory components of many plasmids, which is an overlooked phenomenon that possibly facilitates their dissemination across microbiomes.

microbiology↗

bioRxiv2021

Metagenomic evidence for co-occurrence of antibiotic, biocide and metal resistancegenes in pigs

Antibiotic-resistant pathogens constitute an escalating public health concern. Hence a better understanding of the underlying processes responsible for this expansion is urgently needed. Co-selection of heavy metals/biocides and antibiotic resistance genes (ARGs) has been suggested as one potential mechanism promoting the proliferation of antimicrobial resistance (AMR). This paper aims to elucidate this interplay and exploit differences in antibiotic usage to infer patterns of co-selection by the non-antibiotic factors metals and biocides in the context of pig farming. We examined 278 gut metagenomes from pigs with continuous antibiotic exposure, only at weaning and at no exposure. Metals as growth promoters and biocides as disinfectants are currently used with little restrictions in stock farming. The pigs under continuous antibiotic exposure displayed the highest co-occurrence of ARGs and other genetic elements while the pigs under limited use of antibiotics still showed abundant co-occurrences. Pathogens belonging to Enterobacteriaceae displayed increased co-occurrence phenomena, suggesting that this maintenance is not a random selection process from a mobilized pool but pertains to specific phylogenetic clades. These results suggest that metals and biocides displayed strong selective pressures on ARGs exerted by intensive farming, regardless of the current use of antibiotics. HighlightsO_LIA comprehensive gut microbiome metagenomics analysis of 278 pigs C_LIO_LICo-selection phenomena were investigated via co-occurrence patterns as a proxy C_LIO_LITwenty-seven types of co-occurrences involving 131 resistance genes were detected C_LIO_LIRegardless of use of antibiotics, AMR can be maintained by co-occurrence with MRGs/BRGs C_LIO_LIMaintenance of AMR is not a random selection process but pertains to specific phylogenetic clades C_LI

bioinformatics↗

bioRxiv2020

Extended spectrum β-lactamase and carbapenemase genes are substantially and sequentially reduced during conveyance and treatment of urban sewage

Integrated and quantitative observations of antibiotic resistance genes (ARGs) in urban water systems (UWSs) are lacking. We sampled three UWSs for clinically important extended spectrum {beta}-lactamase (ESBL) and carbapenemase (CP) genes, mobile genetic elements and microbial communities. Sewage - especially from hospitals - carried substantial loads of ESBL and CP genes (106 - 107 per person equivalent), but those loads progressively declined along the UWS, resulting in minimal emissions (101 - 104 copies per person equivalent). Removal was primarily during sewage conveyance (65% {+/-} 36%) rather than within sewage treatment (34% {+/-} 23%). The ARGs clustered in groups based on their persistence; less persistent groups were associated to putative host taxa (especially Enterobacteriaceae and Moraxellaceae), while more persistent groups appear horizontally transferred as they correlated with mobile genetic elements. This first documentation of a substantial ARG reduction during sewage conveyance provides opportunities for antibiotic resistance management and a caution for sewage-based ARG surveillance.

ecology↗

bioRxiv2020

Conjugative dissemination of plasmids in rapid sand filters: a trojan horse strategy to enhance pesticide degradation in groundwater treatment

The supply of clean water for human consumption is being challenged by the appearance of pesticide pollutants in groundwater ecosystems. Biological rapid sand filtration is a commonly employed method for the removal of organic and inorganic impurities in water which relies on the degradative properties of microorganisms for the removal of diverse contaminants, including pesticides. Although sustainable and relatively inexpensive, the bioremediation capabilities of rapid sand filters vary greatly across waterworks. Bioaugmentation efforts with degradation-proficient bacteria have proven difficult due to the inability of the exogenous microbes to stably colonize the sand filters. Pesticide degrading genes, however, are often encoded naturally by plasmids--extrachromosomal DNA elements that can transfer between bacteria--yet their ability to spread within rapid sand filters have remained unknown. To evaluate the potential use of plasmids for the dissemination of pesticide degrading genes, we examined the permissiveness of rapid sand filter communities towards four environmental transmissible plasmids; RP4, RSF1010, pKJK5 and TOL (pWWO), using a dual-fluorescent bioreporter platform combined with FACS and 16S rRNA gene amplicon sequencing. Our results reveal that plasmids can transfer at high frequencies and across distantly related taxa from rapid sand filter communities, emphasizing their suitability for introducing pesticide degrading determinants in the microbiomes of underperforming water purification plants.

microbiology↗

bioRxiv2019

Intra-species DNA exchange: Bacillus subtilis prefers sex with less related strains

B. subtilis is a surface-dwelling bacterium that is competent for natural transformation. Genetically distinct B. subtilis swarms form a boundary upon encounter, mediated by a fast-evolving molecular kin discrimination (KD) system. We here demonstrate that KD-mediated swarm antagonisms in B. subtilis promote transformation-mediated horizontal gene transfer between strains of low relatedness. Gene transfer is largely uni-directional and the result of the induction of competence of the recipient strain by the donor strain is linked to a sigW-mediated stress response. More closely related strains, which in theory would experience more efficient recombination due to increased sequence homology, did not upregulate transformation upon encounter, demonstrating that social interactions can override mechanistic barriers to horizontal gene transfer. KD-mediated competence in response to the encounter of distinct neighbouring strains could maximize the probability of efficient incorporation of novel alleles and genes that have proved to function in a genomically and ecologically similar context.

microbiology↗

bioRxiv2019

Plasmids persist in a microbial community by providing fitness benefit to multiple phylotypes

The current epidemic of antibiotic resistance has been facilitated by the wide and rapid horizontal dissemination of antibiotic resistance genes (ARGs) in microbial communities. Indeed, ARGs are often located on plasmids, which can efficiently shuttle genes across diverse taxa. While the existence conditions of plasmids have been extensively studied in a few model bacterial populations, their fate in complex bacterial communities is poorly understood. Here, we coupled plasmid transfer assays with serial growth experiments to investigate the persistence of the broad-host-range IncP-1 plasmid pKJK5 in microbial communities derived from a sewage treatment plant. The cultivation conditions combined different nutrient and oxygen levels, and were non-selective and non-conducive for liquid-phase conjugal transfer. Following initial transfer, the plasmid persisted in almost all conditions during a 10-day serial growth experiment (equivalent to 60 generations), with a transient transconjugant incidence up to 30%. By combining cell enumeration and sorting with amplicon sequencing, we mapped plasmid fitness effects across taxa of the microbial community. Unexpected plasmid fitness benefits were observed in multiple phylotypes of Aeromonas, Pseudomonas and Enterobacteriaceae, which resulted in community-level plasmid persistence. We demonstrate, for the first time, that plasmid fitness effects across community members can be estimated in a high-throughput way without prior isolation. By gaining a fitness benefit when carrying plasmids, members within complex microbial communities might have a hitherto unrecognized potential to maintain plasmids for long-term community-wide access.

ecology↗

bioRxiv2019

Construction of simplified microbial consortia to degrade recalcitrant materials based on enrichment and dilution-to-extinction cultures

The capacity of microbes degrading recalcitrant materials has been extensively explored from environmental remediation to industrial applications. Although significant achievements were obtained with single strains, focus is now going toward the use of microbial consortia because of advantages in terms of functional stability and efficiency. While consortia assembly attempts were made from several known single strains, another approach consists in obtaining consortia from complex environmental microbial communities in search for novel microbial species, genes and functions. However, assembling efficient microbial consortia from complex environmental communities is far from trivial due to large diversity and biotic interactions at play. Here we propose a strategy containing enrichment and dilution-to-extinction cultures to construct simplified microbial consortia (SMC) for keratinous waste management, from complex environmental communities. Gradual dilutions were performed from a keratinolytic microbial consortium, and dilution 10-9 was selected to construct a SMC library. Further compositional analysis and keratinolytic activity assays demonstrated that microbial consortia were successfully simplified, without impacting their biodegradation capabilities. These SMC possess promising potential for efficient keratinous valorization. More importantly, this reasoning and methodology could be transferred to other topics involving screening for simplified communities for biodegradation, thus considerably broadening its application scope.\n\nImportanceMicrobial consortia have got more and more attention and extensive applications due to their potential advantages. However, a high diversity of microbes is likely to hide uncontrollable risks in practice specific to novel strains and complicated interaction networks. Exploring a convenient and efficient way to construct simplified microbial consortia is able to broaden the applied scope of microbes. This study presents the approach based on enrichment and dilution-to-extinction cultures, which gain abundance microbial consortia including some without losing efficiency from the enriched functional microbial community. The microbial interactions at the strain level were evaluated by using compositional identification and correlation analysis, which contribute to revealing the roles of microbes in the degradation process of recalcitrant materials. Our findings provide a systematic scheme to achieve optimizing microbial consortia for biodegradation from an environmental sample, could be readily applied to a range of recalcitrant materials management from environmental remediation to industrial applications.

microbiology↗