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bioRxiv2017

An RNA Virome Associated To The Golden Orb-Weaver Spider Nephila clavipes

The golden orb-weaver spider Nephila clavipes, known for its sexual size dimorphism, is abundant and widespread in the New World. The first annotated genome of orb-weaver spiders, exploring N. clavipes, has recently been reported. The study, focused primarily on the diversity of silk specific genes, shed light into the complex evolutionary history of spiders. Furthermore, a robust transcriptome analysis provided a massive resource for N. clavipes RNA survey. Here, I present evidence of viral sequences corresponding to the first 10 extant virus species associated to N. clavipes and indeed, nephilids. The putatively new species are linked to ssRNA positive-strand viruses, such as Picornavirales, and to ssRNA negative-strand and dsRNA viruses. In addition, I detected sequence data of new strains of two recently reported arthropod viruses, which complemented and extended the corresponding sequence references. The identified viruses appear to be complete, potentially functional, and presenting the typical architecture and consistent viral domains. The intrinsic nature of the detected sequences and their absence in the recently generated genome assembly, suggest that they correspond to bona fide RNA virus sequences. The available RNA data allowed for the first time to address a tissue/organ specific analysis of virus loads/presence in spiders, suggesting a complex spatial and differential distribution of the tentative viruses, encompassing the spider brain and also silk and venom glands. Until recently, the virus landscape associated to spiders remained elusive. The discovered viruses described here provide only a fragmented glimpse of the potential magnitude of the Aranea virosphere. Future studies should focus not only on complementing and expanding these findings, but also on addressing the potential ecological role of these viruses, which might influence the biology of these outstanding arthropod species.\n\nFunding statementThe author received no specific funding for this study.\n\nEthics statements(Authors are required to state the ethical considerations of their study in the manuscript, including for cases where the study was exempt from ethical approval procedures)

microbiology↗

bioRxiv2017

Rob And MarA Alter Susceptibility Of Escherichia coli To Antibiotics In Presence Of Salicylate

When exposed to stress, bacterial cells launch a diverse response to enhance their chances of survival. This response involves modulation of expression of a large number of proteins which help the cell counter stress. This modulation is facilitated by several transcription factors in bacteria and in E. coli three homologous regulators, MarA, Sox, and Rob are known to launch a coordinated response to combat various stress environments. MarA and SoxS are known to control multiple antibiotic resistance and superoxide regulon respectively. Rob has been observed to control similar downstream targets as MarA and SoxS. However, physiological relevance of Rob in not understood. We show that Rob along with MarA, in presence of inducer salicylate, can help cell survive in presence of lethal concentration of wide range of antibiotics.

microbiology↗

bioRxiv2017

Nucleus Specific Expression In The Multinucleated Mushroom-Forming Fungus Agaricus bisporus Reveals Different Nuclear Regulatory Programs

MotivationFungi are essential in nutrient recycling in nature. They also form symbiotic, commensal, parasitic and pathogenic interactions with other organisms including plants, animals and humans. Many fungi are polykaryotic, containing multiple nuclei per cell. In the case of heterokaryons, there are even different nuclear types within a cell. It is unknown what the different nuclear types contribute in terms of mRNA expression levels in fungal heterokaryons. Each cell of the cultivated, mushroom forming basidiomycete Agaricus bisporus contains 2 to 25 nuclei of two nuclear types, P1 or P2, that originate from two parental strains. Using RNA-Seq data, we wish to assess the differential mRNA contribution of individual nuclear types in heterokaryotic cells and its functional impact.\n\nResultsWe studied differential expression between genes of the two nuclear types throughout mushroom development of A. bisporus in various tissue types. The two nuclear types, produced specific mRNA profiles which changed through development of the mushroom. The differential regulation occurred at a gene and multi-gene locus level, rather than the chromosomal or nuclear level. Although the P1 nuclear type dominates the mRNA production throughout development, the P2 type showed more differentially upregulated genes in important functional groups including genes involved in metabolism and genes encoding secreted proteins. Out of 5,090 karyolelle pairs, i.e. genes with different alleles in the two nuclear types, 411 were differentially expressed, of which 246 were up-regulated by the P2 type. In the vegetative mycelium, the P2 nucleus up-regulated almost three-fold more metabolic genes and cazymes than P1, suggesting phenotypic differences in growth. A total of 10% of the differential karyollele expression is associated with differential methylation states, indicating that epigenetic mechanisms may be partly responsible for nuclear specific expression.\n\nConclusionWe have identified widespread transcriptomic variation between the two nuclear types of A. bisporus. Our novel method enables studying karyollelle specific expression which likely influences the phenotype of a fungus in a polykaryotic stage. This is thus relevant for the performance of these fungi as a crop and for improving this species for breeding. Our findings could have a wider impact to better understand fungi as pathogens. This work provides the first insight into the transcriptomic variation introduced by genomic nuclear separation.

microbiology↗

bioRxiv2017

The Nucleoid Occlusion Protein SlmA Is A Direct Transcriptional Activator Of Chitobiose Utilization In Vibrio cholerae

Chitin utilization by the cholera pathogen Vibrio cholerae is required for its persistence and evolution via horizontal gene transfer in the marine environment. Genes involved in the uptake and catabolism of the chitin disaccharide chitobiose are encoded by the chb operon. The orphan sensor kinase ChiS is critical for regulation of this locus, however, the mechanisms downstream of ChiS activation that result in expression of the chb operon are poorly understood. Using an unbiased transposon mutant screen, we uncover that the nucleoid occlusion protein SlmA is a regulator of the chb operon. SlmA has not previously been implicated in gene regulation. Also, SlmA is a member of the TetR family of proteins, which are generally transcriptional repressors. In vitro, we find that SlmA binds directly to the chb operon promoter, and in vivo, we show that this interaction is, surprisingly, required for transcriptional activation of this locus and for chitobiose utilization. Using point mutations that disrupt distinct functions of SlmA, we find that DNA-binding, but not nucleoid occlusion, is critical for transcriptional activation. This study identifies a novel role for SlmA as a transcriptional regulator in V. cholerae in addition to its established role as a cell division licensing factor.\n\nAUTHOR SUMMARYThe cholera pathogen Vibrio cholerae is a natural resident of the aquatic environment and causes disease when ingested in the form of contaminated food or drinking water. In the aquatic environment, the shells of marine zooplankton, which are primarily composed of chitin, serve as an important food source for this pathogen. The genes required for the utilization of chitin are tightly regulated in V. cholerae, however, the exact mechanism underlying this regulation is currently unclear. Here, we uncover that a protein involved in regulating cell division is also important for regulating the genes involved in chitin utilization. This is a newly identified property for this cell division protein and the significance of a common regulator for these two disparate activities remains to be understood.

microbiology↗

bioRxiv2017

Inter-individual Recovery Of The Microbiota And Metabolome Over Time Following Fecal Microbiota Transplantation In Patients With Recurrent Clostridium difficile Infection

A significant proportion of individuals develop recurrent Clostridium difficile infection (CDI) following initial disease. Fecal microbiota transplantation (FMT), a highly effective treatment method for recurrent CDI, has been demonstrated to induce microbiota recovery, a critical component of disease recovery. However, identification of the specific microbes and their functions that directly impact recovery from CDI remains difficult. We assessed for associations among microbial community members and metabolites in patients with recurrent CDI following treatment with FMT over time to identify groups of bacteria with potential restorative functions. Using 16S rRNA gene-based sequencing, we observed marked similarity of the microbiota between recipients following FMT (n = 6, sampling up to 6 months post-FMT) and their respective donors. Increased levels of the secondary bile acid deoxycholic acid and the short chain fatty acids (SCFAs) butyrate, acetate, and propionate were observed post-FMT. To take into account longitudinal sampling and intra-individual differences, we applied a generalized estimating equation approach to model metabolite concentrations with the presence of specific members of the microbiota. Microbial metabolites that were increased following FMT associated with members classified within the Lachnospiraceae, Ruminococcaceae, and unclassified Clostridiales families. In contrast, members of these taxa were inversely associated with primary bile acids. The longitudinal aspect of this study allowed us to characterize individualized patterns of recovery, revealing variability between and within patients following FMT.\n\nIMPORTANCEClostridium difficile infection (CDI) is an urgent and serious healthcare-associated problem. In recent years, fecal microbiota transplantation (FMT) has been successfully used to treat recurrent CDI, a frequent outcome of disease. While it is apparent that FMT promotes recovery of the microbiota, it is unclear how microbes and their functions promote recovery from disease. This study aimed to identify associations among microbes and metabolites following FMT and to identify critical microbial functions following FMT treatment for recurrent CDI. Overall, recovery of the metabolome was highly dynamic and individualized in all patients, who were all successfully treated. Our results suggest that microbial changes following FMT may be highly specific to the donor-recipient relationship. Further understanding of the host-microbe environments necessary to enable successful transplantation of microbes during FMT could aid development of specific microbial therapeutics for recurrent CDI and other gastrointestinal diseases.

microbiology↗

bioRxiv2017

Human Migration And The Spread Of Malaria Parasites To The New World

BackgroundThe Americas were the last continent to be settled by modern humans, but how and when human malaria parasites arrived in the New World is uncertain. Here, we apply phylogenetic analysis and coalescent-based gene flow modeling to a global collection of Plasmodium falciparum and P. vivax mitogenomes to infer the demographic history and geographic origins of malaria parasites circulating in the Americas. Importantly, we examine P. vivax mitogenomes from previously unsampled forest-covered sites along the Atlantic Coast of Brazil, including the vivax-like species P. simium that locally infects platyrrhini monkeys.\n\nResultsThe best-supported gene flow models are consistent with migration of both malaria parasites from Africa and South Asia to the New World, with no genetic signature of a population bottleneck upon parasite's arrival in the Americas. We found evidence of additional gene flow from Melanesia in P. vivax (but not P. falciparum) mitogenomes from the Americas and speculate that some P. vivax lineages might have arrived with the Australasian peoples who contributed genes to Native Americans in pre-Columbian times. Mitochondrial haplotypes characterized in P. simium from monkeys from the Atlantic Forest are shared by local humans. These vivax-like lineages have not spread to the Amazon Basin, are much less diverse than P. vivax circulating elsewhere in Brazil, and show no close genetic relatedness with P. vivax populations from other continents.\n\nConclusionsEnslaved peoples brought from a wide variety of African locations were major carriers of P. falciparum mitochondrial lineages into the Americas, but additional human migration waves are likely to have contributed to the extensive genetic diversity of present-day New World populations of P. vivax. The reduced genetic diversity of vivax-like monkey parasites, compared with human P. vivax from across this country, argues for a recent human-to-monkey transfer of these lineages in the Atlantic Forest of Brazil.\n\nAuthor summaryMalaria is currently endemic to the Americas, with over 400,000 laboratory-confirmed infections reported annually, but how and when human malaria parasites entered this continent remains largely unknown. To determine the geographic origins of malaria parasites currently circulating in the Americas, we examined a global collection of Plasmodium falciparum and P. vivax mitochondrial genomes, including those from understudied isolates of P. vivax and P. simium, a vivax-like species that infect platyrrhini monkeys, from the Atlantic Forest of Brazil. We found evidence of significant historical migration to the New World of malaria parasites from Africa and, to a lesser extent, South Asia, with further genetic contribution of Melanesian lineages to South American P. vivax populations. Importantly, mitochondrial haplotypes of P. simium are shared by monkeys and humans from the Atlantic Forest, most likely as a result of a recent human-to-monkey transfer. Interestingly, these potentially zoonotic lineages are not found in the Amazon Basin, the main malaria-endemic area in the Americas. We conclude that enslaved Africans were the main carriers of P. falciparum mitochondrial lineages into the Americas, whereas additional migration waves of Australasian peoples and parasites may have contributed to the genetic makeup of present-day New World populations of P. vivax.

microbiology↗

bioRxiv2017

Use Of RetroNectin In Studies Requiring In Vitro HIV Infection Of Human Hematopoietic Stem/Progenitor Cells

Human immunodeficiency virus (HIV) causes damage, directly or indirectly, to the whole hematopoietic system including CD34+ hematopoietic stem/progenitor cells (HSPC). CXCR4-tropic strains of HIV-1 may be potent to affect the function of CD34+CXCR4+ progenitor cells either by infecting the cells or by modifying the dynamics of more differentiated hematopoietic cells. However, CD34+ cells are known for the resistance to HIV-1 infection in vitro, restricting the detailed analysis of the impact of HIV upon HSPC. Here the authors report a use of RetroNectin, a recombinant fibronectin fragment used for gene transfer with lentiviral vectors, to overcome the limitation.

microbiology↗

bioRxiv2017

HIV Persistence Alters CXCR4 Expression Patterns In OP9-DL1-Mediated Differentiation Of In Vitro Infected Human Cord Blood CD34+ Cells

HIV-1 causes the loss of CD4+ T cells via depletion or impairment of their production. The latter involves infection of thymocytes, but the involvement of other cells including haematopoietic CD34+ cells remains unclear even though HIVpositive patients frequently manifest myelosuppression. In this study, we utilised the OP9-DL1 coculture system, which supports in vitro T-lineage differentiation of human haematopoietic stem/progenitor cells. Cord-derived CD34+ cells were infected with CXCR4-tropic HIV-1NL4-3 and cocultured. HIV-infected cocultures exhibited sustained viral replication for 5 weeks, as well as reduced CD4+ T-cell growth at weeks 3-5. We further revealed that CD34+CD7+CXCR4+ cells can be quickly depleted as early as in 1 week after infection of the subset, and this was accompanied by the emergence of CD34+CD7+CD4+ cells. These results indicate that CXCR4-tropic HIV-1 strains may disrupt CD34+CD7+ lymphoid progenitor cell pools, presumably leading to impaired T-cell production potential.

microbiology↗

bioRxiv2017

Specific Virus-Host Genome Interactions Revealed By Tethered Chromosome Conformation Capture

Viruses have evolved a variety of mechanisms to interact with host cells for their adaptive benefits, including subverting host immune responses and hijacking host DNA replication/transcription machineries [1-3]. Although interactions between viral and host proteins have been studied extensively, little is known about how the vial genome may interact with the host genome and how such interactions could affect the activities of both the virus and the host cell. Since the three-dimensional organization of a genome can have significant impact on genomic activities such as transcription and replication, we hypothesize that such structure-based regulation of genomic functions also applies to viral genomes depending on their association with host genomic regions and their spatial locations inside the nucleus. Here, we used Tethered Chromosome Conformation Capture (TCC) to investigate viral-host genome interactions between the adenovirus and human lung fibroblast cells. We found viral-host genome interactions were enriched in certain active chromatin regions and chromatin domains marked by H3K27me3. The contacts by viral DNA seems to impact the structure and function of the host genome, leading to remodeling of the fibroblast epigenome. Our study represents the first comprehensive analysis of viral-host interactions at the genome structure level, revealing unexpectedly specific virus-host genome interactions. The non-random nature of such interactions indicates a deliberate but poorly understood mechanism for targeting of host DNA by foreign genomes.

microbiology↗

bioRxiv2017

Phosphate Is The Third Nutrient Monitored By TOR In Candida albicans And Provides A Target For Fungal-Specific Indirect TOR Inhibition

The TOR pathway regulates morphogenesis and responses to host cells in the fungal pathogen Candida albicans. Eukaryotic TOR complex 1 (TORC1) induces growth and proliferation in response to nitrogen and carbon source availability. Our unbiased genetic approach seeking new components of TORC1 signaling in C. albicans revealed that the phosphate transporter Pho84 is required for normal TORC1 activity. We found that mutants in PHO84 are hypersensitive to rapamycin and, in response to phosphate feeding, generate less phosphorylated ribosomal protein S6 (P-S6) than wild type. The small GTPase Gtr1, a component of the TORC1-activating EGO complex, links Pho84 to TORC1. Mutants in Gtr1, but not in another TORC1-activating GTPase, Rhb1, are defective in the P-S6 response to phosphate. Overexpression of Gtr1 and of a constitutively active Gtr1Q67L mutant suppress TORC1-related defects. In S. cerevisiae pho84 mutants, constitutively active Gtr1 suppresses a TORC1 signaling defect but does not rescue rapamycin hypersensitivity. Hence connections from phosphate homeostasis to TORC1 may differ between C. albicans and S. cerevisiae. The converse direction of signaling, from TORC1 to the phosphate homeostasis (PHO) regulon, previously observed in S. cerevisiae, was genetically demonstrated in C. albicans using conditional TOR1 alleles. A small molecule inhibitor of Pho84, an FDA-approved drug, inhibits TORC1 signaling and potentiates the activity of the antifungals amphotericin B and micafungin. Anabolic TORC1-dependent processes require significant amounts of phosphate. Our study demonstrates that phosphate availability is monitored and also controlled by TORC1, and that TORC1 can be indirectly targeted by inhibiting Pho84.\n\nSignificanceThe human fungal pathogen Candida albicans uses the TOR signaling pathway to contend with varying host environments and thereby regulate cell growth. Seeking novel components of the C. albicans TOR pathway we identified a cell-surface phosphate importer, Pho84, and its molecular link to TOR complex 1 (TORC1). Since phosphorus is a critical element for anabolic processes like DNA replication, ribosome biogenesis, translation and membrane biosynthesis, TORC1 monitors its availability in regulating these processes. By depleting the central kinase in the TORC1 pathway, we showed that TORC1 signaling modulates regulation of phosphate acquisition. An FDA-approved small-molecule inhibitor of Pho84 inhibits TORC1 signaling and potentiates the activity of the gold-standard antifungal amphotericin B and the echinocandin micafungin.

microbiology↗

bioRxiv2017

Inoculation Of Biocontrol Bacteria Alleviated Panax ginseng Replanting Problem

Replanting problem is a common and serious issue hindering the continuous cultivation of Panax plants. Changes in soil microbial community driven by plant species of different ages and developmental stages are speculated to cause this problem. Inoculation of microbial antagonists is proposed to alleviate replanting issues efficiently.\n\nHigh-throughput sequencing revealed that bacterial diversity evidently decreased, and fungal diversity markedly increased in soils of adult ginseng plants in the root growth stage. Relatively few beneficial microbe agents, such as Luteolibacter, Cytophagaceae, Luteibacter, Sphingomonas, Sphingomonadaceae, and Zygomycota, were observed. On the contrary, the relative abundance of harmful microorganism agents, namely, Brevundimonas, Enterobacteriaceae, Pandoraea, Cantharellales, Dendryphion, Fusarium, and Chytridiomycota, increased with pant age. Furthermore, Bacillus subtilis 50-1 was isolated and served as microbial antagonists against pathogenic Fusarium oxysporum of ginseng root-rot, and its biocontrol efficacy was 67.8% using a dual culture assay. The ginseng death rate and relative abundance of Fusarium decreased by 63.3% and 46.1%, respectively, after inoculation with 50-1 in replanting soils. Data revealed that changes in the diversity and composition of rhizospheric microbial communities driven by ginseng of different ages and developmental stages could cause microecological degradation. Biocontrol using microbial antagonists was an effective method for alleviating the replanting problem.\n\nHighlightChanges in rhizospheric microbial communities driven by ginseng plants 13 of different ages and developmental stages could cause microecological degradation. 14 Biocontrol using microbial antagonists effectively alleviated the replanting problem.

microbiology↗

bioRxiv2017

Plasmids, Viruses, And Other Circular Elements In Rat Gut

Circular DNA such as plasmids and some viruses is the major source of genetic variation in bacteria and thus has the same important evolutionary function as sexual reproduction in eukaryotic species: It allows dissemination of advantageous traits through bacterial populations. Here, we present the largest collection of novel complete extrachromosomal genetic elements to date, and compare the diversity, distribution, and content of circular sequences from 12 rat cecum samples from the pristine Falkland Islands and Danish hospital sewers, two environments with contrasting anthropogenic impact. Using a validated pipeline, we find 1,869 complete, circular, non-redundant sequences, of which only 114 are previously described. While sequences of similar size from the two environments share general features, the size distribution of the elements between environments differs significantly, with hospital sewer samples hosting larger circular elements than Falkland Island samples, a possible consequence of the massive anthropogenic influence in the hospital sewer environment. Several antibiotic resistance genes have been identified with a notably larger diversity in hospital sewer samples than in Falkland Islands samples in concordance with expectations. Our findings suggest that even though sequences of similar length carry similar traits, the mobilome of rat gut bacteria are affected by human activities in that sewer rats have larger elements and more diverse large elements than pristine island rats. More than 1000 novel and not classified small sequences was identified and hint the existence of a biological unit not previously described on a community level.\n\nList of figures O_LISampling sites and Rat gut anatomy\nC_LIO_LIRarefaction curves of circular elements\nC_LIO_LIElements shared between environments\nC_LIO_LISize distribution plots of rep, mob, stab, capsid carrying elements.\nC_LIO_LIGraphical representation of representative elements\nC_LIO_LIReplication genes content, diversity\nC_LIO_LIRep_2 plasmid replication gene phylogeny\nC_LIO_LITable Resfams findings\nC_LI\n\nList of appendices O_LIbasic statistics table\nC_LIO_LIPhylogeny of plasmid replication genes\nC_LIO_LIList of known plasmids and circular sequences found in 1869 elements\nC_LIO_LIAutomatic identification of identical circular elements with different breaking points\nC_LIO_LITest of separation of plasmids and viruses based on predicted, annotated genes\nC_LIO_LINo false positive circular sequences from MG1655 genomic sequencing.\nC_LI

microbiology↗

bioRxiv2017

Influence Of Non-Metabolic Microbial Growth Promotors (AMP Activators) On The Sensitivity To Antimicrobials In The Actually Multiresistant Microbial Strains

IntroductionThe control over multi-resistant nosocomial strains of microorganisms has been becoming increasingly urgent in recent years. We suggest a new paradigm that eliminates killing or inhibiting the growth of bacteria. Excluding bacteria death supresses the selection of resistant strains of microorganisms. We have developed such non-metabolite growth promoters, which in very low doses stimulate the rapid growth of many bacteria strains. The mechanism of action of the enhancers is caused by the activation of the cAMP high doses accumulation process in the microbial cells. cAMP itself is a substrate for phosphorylation including DNA polymerases.\n\nMaterials and methodsThe susceptible culture collection resistance strains Pseudomonas aeruginosa MDR Kharkov IMI1, Acinetobacter baumanii MDR Kharkov-IMI1, and Clebsiella pneumonia MDR Kharkov-IMI1 were used. The following antimicrobial agents of known potency were evaluated: ciprofloxacin, polymyxin, amikacin. The same broth, but containing 0.001% enhancers (under patenting), has been used for further passaging for MDR strains. Characteristics of bacterial growth were determined in a medium compared at the control group - the broth without enhancers.\n\nResults and discussionEnhancers contribute to a significant increase in the antimicrobial sensitivity to polymyxin, ciprofloxacin and amikacin in multi-resistant strains of bacteria. Changes in the growth characteristics and antimicrobial sensitivity are observed only in the second passage that demonstrates the need for the further studies of the molecular mechanisms of the cAMP effect on the division and growth of microbial cells.

microbiology↗

bioRxiv2017

Genome-Wide Comparison Of Toxigenic And Non-Toxigenic Corynebacterium diphtheriae Isolates Identifies Differences In The Pan Genomes Between Respiratory And Cutaneous Strains

ObjectivesCorynebacterium diphtheriae is the main etiological agent of diphtheria, a global disease causing life-threatening infections, particularly in infants and children. Vaccination with diphtheria toxoid protects against infection with potent toxin producing strains. However a growing number of apparently non-toxigenic but potentially invasive C. diphtheriae strains are identified in countries with low prevalence of diphtheria, raising key questions about genomic structures and population dynamics of the species.\n\nMethodsThis study examined genomic diversity among 47 C. diphtheriae isolates collected in Australia over a 10-year period using whole genome sequencing. Phylogeny was determined using SNP-based mapping and genome wide analysis.\n\nResultsC. diphtheriae sequence type (ST) 32, a non-toxigenic ST with evidence of enhanced virulence that is also circulating in Europe, appears to be endemic in Australia. Isolates from temporospatially related patients displayed the same ST and similarity in their core genomes. The genome-wide analysis highlighted a role of pilins, adhesion factors and iron utilization in infections caused by toxigenic as well as non-toxigenic strains.\n\nConclusionsThe genomic diversity of toxigenic and non-toxigenic strains of C. diphtheriae in Australia suggests multiple local and overseas sources of infection and colonisation. Our findings suggest that regular genomic surveillance of co-circulating toxigenic and non-toxigenic C. diphtheriae can deliver highly nuanced data in order to inform targeted public health actions and policy for predicting the future impact of this highly successful pathogen.

microbiology↗

bioRxiv2017

Recipient-Biased Competition For A Cross-Fed Nutrient Is Required For Coexistence Of Microbial Mutualists

Many mutualistic microbial relationships are based on nutrient cross-feeding. Traditionally, cross-feeding is viewed as being unidirectional from the producer to the recipient. This is likely true when a producers metabolic waste, such as fermentation products, provides carbon for a recipient. However, in some cases the cross-fed nutrient holds value for both the producer and the recipient. In such cases, there is potential for nutrient reacquisition by producer cells in a population, leading to competition against recipients. Here we investigate the consequences of inter-partner competition for cross-fed nutrients on mutualism dynamics using an anaerobic coculture pairing fermentative Escherichia coli and phototrophic Rhodopseudomonas palustris. In this coculture, E. coli excretes waste organic acids that provide carbon for R. palustris. In return, R. palustris cross-feeds E. coli ammonium (NH4+), a valuable nitrogen compound that both species prefer. To explore the potential for inter-partner competition, we first used a kinetic model to simulate cocultures with varied affinities for NH4+ in each species. The model predicted that inter-partner competition for cross-fed NH4+ could profoundly impact population dynamics. We then experimentally tested the predictions by culturing mutants lacking NH4+ transporters in both NH4+ competition assays and cooperative cocultures. Both theoretical and experimental results indicated that the recipient must have a competitive advantage in acquiring valuable cross-fed NH4+ to avoid collapse of the mutualism. Thus, the very metabolites that form the basis for cooperative cross-feeding can also be subject to competition between mutualistic partners.\n\nSignificanceMutualistic relationships, particularly those based on nutrient cross-feeding, promote stability of diverse ecosystems and drive global biogeochemical cycles. Cross-fed nutrients within these systems can be either waste products valued only by one partner or nutrients that both partners value. Here, we explore how inter-partner competition for a communally-valuable cross-fed nutrient impacts mutualism dynamics. We discovered that mutualism stability necessitates that the recipient have a competitive advantage against the producer in obtaining the cross-fed nutrient. We propose that the requirement for recipient-biased competition is a general rule for mutualistic coexistence based on the transfer of communally valuable resources, microbial or otherwise.

microbiology↗

bioRxiv2017

Genome-Enabled Insights Into The Ecophysiology Of The Comammox Bacterium Candidatus Nitrospira nitrosa

The recently discovered comammox bacteria have the potential to completely oxidize ammonia to nitrate. These microorganisms are part of the Nitrospira genus and are present in a variety of environments, including Biological Nutrient Removal (BNR) systems. However, the physiological traits within and between comammox- and nitrite oxidizing bacteria (NOB)-like Nitrospira species have not been analyzed in these ecosystems. In this study, we identified Nitrospira strains dominating the nitrifying community of a sequencing batch reactor (SBR) performing BNR under micro-aerobic conditions. We recovered metagenomes-derived draft genomes from two Nitrospira strains: (1) Nitrospira sp. UW-LDO-01, a comammox-like organism classified as Candidatus Nitrospira nitrosa, and (2) Nitrospira sp. UW-LDO-02, a nitrite oxidizing strain belonging to the Nitrospira defluvii species. A comparative genomic analysis of these strains with other Nitrospira-like genomes identified genomic differences in Ca. Nitrospira nitrosa mainly attributed to each strains niche adaptation. Traits associated with energy metabolism also differentiate comammox from NOB-like genomes. We also identified several transcriptionally regulated adaptive traits, including stress tolerance, biofilm formation and micro-aerobic metabolism, which might explain survival of Nitrospira under multiple environmental conditions. Overall, our analysis expanded our understanding of the genetic functional features of Ca. Nitrospira nitrosa, and identified genomic traits that further illuminate the phylogenetic diversity and metabolic plasticity of the Nitrospira genus.

microbiology↗

bioRxiv2017

Biogeography & Environmental Conditions Shape Phage & Bacteria Interaction Networks Across The Human Microbiome

Viruses and bacteria are critical components of the human microbiome and play important roles in health and disease. Most previous work has relied on studying bacteria and viruses independently, thereby reducing them to two separate communities. Such approaches are unable to capture how these microbial communities interact, such as through processes that maintain community robustness or allow phage-host populations to co-evolve. We implemented a network-based analytical approach to describe phage-bacteria network diversity throughout the human body. We built these community networks using a machine learning algorithm to predict which phages could infect which bacteria in a given microbiome. Our algorithm was applied to paired viral and bacterial metagenomic sequence sets from three previously published human cohorts. We organized the predicted interactions into networks that allowed us to evaluate phage-bacteria connectedness across the human body. We observed evidence that gut and skin network structures were person-specific and not conserved among cohabitating family members. High-fat diets appeared to be associated with less connected networks. Network structure differed between skin sites, with those exposed to the external environment being less connected and likely more susceptible to network degradation by microbial extinction events. This study quantified and contrasted the diversity of virome-microbiome networks across the human body and illustrated how environmental factors may influence phage-bacteria interactive dynamics. This work provides a baseline for future studies to better understand system perturbations, such as disease states, through ecological networks.\n\nAuthor SummaryThe human microbiome, the collection of microbial communities that colonize the human body, is a crucial component to health and disease. Two major components of the human microbiome are the bacterial and viral communities. These communities have primarily been studied separately using metrics of community composition and diversity. These approaches have failed to capture the complex dynamics of interacting bacteria and phage communities, which frequently share genetic information and work together to maintain ecosystem homestatsis (e.g. kill-the-winner dynamics). Removal of bacteria or phage can disrupt or even collapse those ecosystems. Relationship-based network approaches allow us to capture this interaction information. Using this network-based approach with three independent human cohorts, we were able to present an initial understanding of how phage-bacteria networks differ throughout the human body, so as to provide a baseline for future studies of how and why microbiome networks differ in disease states.

microbiology↗

bioRxiv2017

Morphological And Transcriptomic Evidence For Ammonium Induction Of Sexual Reproduction In Thalassiosira pseudonana And Other Centric Diatoms

The reproductive strategy of diatoms includes asexual and sexual phases, but in many species, including the model centric diatom Thalassiosira pseudonana, sexual reproduction has never been observed. Furthermore, the environmental factors that trigger sexual reproduction in diatoms are not understood. Although genome sequences of a few diatoms are available, little is known about the molecular basis for sexual reproduction. Here we show that ammonium reliably induces the key sexual morphologies, including oogonia, auxospores, and spermatogonia, in two strains of T. pseudonana, T. weissflogii, and Cyclotella cryptica. RNA sequencing revealed 1,274 genes whose expression patterns changed when T. pseudonana was induced into sexual reproduction by ammonium. Some of the induced genes are linked to meiosis or encode flagellar structures of heterokont and cryptophyte algae. The identification of ammonium as an environmental trigger suggests an unexpected link between diatom bloom dynamics and strategies for enhancing population genetic diversity.

microbiology↗