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bioRxiv2017

Bacterial lipopolysaccharide reduces the stability of avian and human influenza viruses

Commensal bacteria can promote or reduce the severity of viral infection and disease progression in their hosts depending on the specific viral pathogen1. Influenza A virus (IAV) has a broad host-range, comprises many subtypes, and utilizes different routes of transmission including the fecal-oral route in wild birds2. It has been previously demonstrated that commensal bacteria can interact with the hosts immune system to protect against IAV pathogenesis3,4. However, it is unclear whether bacteria and their products may be interacting directly with IAV to impact virion stability. Herein we show that gastrointestinal (GI) tract bacterial isolates in an in vitro system significantly reduce the thermal stability of IAV. Moreover, bacterial lipopolysaccharide (LPS), found on the exterior surfaces of bacteria, was sufficient to significantly decrease the stability of both human and avian viral strains at the physiological temperatures of their respective hosts, as well as in the aquatic environment. Subtype and host-origin of the viruses were shown to affect the extent to which IAV was susceptible to LPS. Furthermore, using a receptor-binding assay and transmission electron microscopy, we observed that LPS binds to and affects the morphology of influenza virions.

microbiology↗

bioRxiv2017

Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate-reducing benthic microbial populations

Conflict of interestThe authors declare no conflict of interest.\n\nShort summaryFermentation coupled to sulfate reduction is a globally important process for the remineralization of organic carbon in marine sediments. The present study uses long-term, replicated continuous culture bioreactors and meta-omics to investigate the ecophysiology of the involved microbial populations at an unprecedented resolution. We reveal complex trophic networks, in which fermenters and sulfate reducers coexist with nitrate- and oxygen respirers, we indicate strategies and niches of the microbial populations, and describe a novel and widespread, yet uncultured fermentative organism. These insights are crucial to understand fermentation coupled to sulfate reduction and relevant to assess microbial dynamics and community-level responses in coastal ecosystems.\n\nFor the anaerobic remineralization of organic matter in marine sediments, sulfate reduction coupled to fermentation plays a key role. Here, we enriched sulfate-reducing/fermentative communities from intertidal sediments under defined conditions in continuous culture. We transiently exposed the cultures to oxygen or nitrate twice daily and investigated the community response. Chemical measurements, provisional genomes and transcriptomic profiles revealed trophic networks of microbial populations. Sulfate reducers coexisted with facultative nitrate reducers or aerobes enabling the community to adjust to nitrate or oxygen pulses. Exposure to oxygen and nitrate impacted the community structure, but did not suppress fermentation or sulfate reduction as community functions, highlighting their stability under dynamic conditions. The most abundant sulfate reducer in all cultures, related to Desulfotignum balticum, appeared to have coupled acetate oxidation to sulfate reduction. We described a novel representative of the widespread uncultured phylum Candidatus Fermentibacteria (formerly candidate division Hyd24-12). For this strictly anaerobic, obligate fermentative bacterium, we propose the name Ca. \"Sabulitectum silens\" and identify it as a partner of sulfate reducers in marine sediments. Overall, we provide insights into the metabolic network of fermentative and sulfate-reducing microbial populations, their niches, and adaptations to a dynamic environment.

microbiology↗

bioRxiv2017

COREMIC: a web-tool to search for a root-zone associated CORE MICrobiome

Microbial diversity on earth is extraordinary, and soils alone harbor thousands of species per gram of soil. Understanding how this diversity is sorted and selected into habitat niches is a major focus of ecology and biotechnology, but remains only vaguely understood. A systems-biology approach was used to mine information from databases to show how it can be used to answer questions related to the core microbiome of habitat-microbe relationships. By making use of the burgeoning growth of information from databases, our tool \"COREMIC\" meets a great need in the search for understanding niche partitioning and habitat-function relationships. The work is unique, furthermore, because it provides a user-friendly statistically robust web-tool (http://coremic2.appspot.com), developed using Google App Engine, to help in the process of database mining to identify the \"core microbiome\" associated with a given habitat. A case study is presented using data from 31 switchgrass rhizosphere community habitats across a diverse set of soil and sampling environments. The methodology utilizes an outgroup of 28 non-switchgrass (other grasses and forbs) to identify a core switchgrass microbiome. Even across a diverse set of soils (5 environments), and conservative statistical criteria (presence in more than 90% samples and FDR q-val < 0.05% for Fishers exact test) a core set of bacteria associated with switchgrass was observed. These included, among others, closely related taxa from Lysobacter spp., Mesorhizobium spp, and Chitinophagaceae. These bacteria have been shown to have functions related to the production of bacterial and fungal antibiotics and plant growth promotion. COREMIC can be used as a hypothesis generating or confirmatory tool that shows great potential for identifying taxa that may be important to the functioning of a habitat (e.g. host plant). The case study, in conclusion, shows that COREMIC can identify key habitat-specific microbes across diverse samples, using currently available databases and a unique freely available software.

microbiology↗

bioRxiv2017

Unleashing natural competence in Lactococcus lactis by induction of the competence regulator ComX

In biotechnological work horses like Streptococcus thermophilus and Bacillus subtilis natural competence can be induced, which facilitates genetic manipulation of these microbes. However, in strains of the important dairy starter Lactococcus lactis natural competence has not been established to date. However, in silico analysis of complete genome sequences of 43 L. lactis strains revealed complete late-competence gene-sets in 2 L. lactis subspecies cremoris strains (KW2 and KW10) and 8 L. lactis subspecies lactis strains, including the model strain IL1403 and the plant-derived strain KF147. The remainder of the strains, including all dairy isolates, displayed genomic decay in one or more of the late competence genes. Nisin-controlled expression of the competence regulator comX in L. lactis subsp. lactis KF147 resulted in the induction of expression of the canonical competence regulon, and elicited a state of natural competence in this strain. By contrast, comX expression in L. lactis NZ9000, predicted to encode an incomplete competence gene-set, failed to induce natural competence. Moreover, mutagenesis of the comEA-EC operon in strain KF147, abolished the comX driven natural competence, underpinning the involvement of the competence machinery. Finally, introduction of nisin-inducible comX expression into nisRK-harboring derivatives of strains IL1403 and KW2 allowed the induction of natural competence also in these strains, expanding this phenotype to other L. lactis strains of both subspecies.\n\nSignificance statementSpecific bacterial species are able to enter a state of natural competence in which DNA is taken up from the environment, allowing the introduction of novel traits. Strains of the species Lactococcus lactis are very important starter cultures for the fermentation of milk in the cheese production process, where these bacteria contribute to the flavor and texture of the end-product. The activation of natural competence in this industrially relevant organism can accelerate research aiming to understand industrially relevant traits of these bacteria, and can facilitate engineering strategies to harness the natural biodiversity of the species in optimized starter strains.

microbiology↗

bioRxiv2017

ComM is a hexameric helicase that promotes branch migration during natural transformation in diverse Gram-negative species

Acquisition of foreign DNA by natural transformation is an important mechanism of adaptation and evolution in diverse microbial species. Here, we characterize the mechanism of ComM, a broadly conserved AAA+ protein previously implicated in homologous recombination of transforming DNA (tDNA) in naturally competent Gram-negative bacterial species. In vivo, we found that ComM was required for efficient comigration of linked genetic markers in Vibrio cholerae and Acinetobacter baylyi, which is consistent with a role in branch migration. Also, ComM was particularly important for integration of tDNA with increased sequence heterology, suggesting that its activity promotes the acquisition of novel DNA sequences. In vitro, we showed that purified ComM binds ssDNA, oligomerizes into a hexameric ring, and has bidirectional helicase and branch migration activity. Based on these data, we propose a model for tDNA integration during natural transformation. This study provides mechanistic insight into the enigmatic steps involved in tDNA integration and uncovers the function of a protein required for this conserved mechanism of horizontal gene transfer.

microbiology↗

bioRxiv2017

Engagement rules that underpin DBL-DARC interactions for ingress of Plasmodium knowlesi and Plasmodium vivax into human erythrocytes

The molecular mechanisms by which P. knowlesi and P. vivax invade human red blood cells have long been studied. Malaria parasite erythrocytic stages comprise of repeated bursts of parasites via cyclical invasion of host RBCs using dedicated receptor-ligand interactions. A family of erythrocyte-binding proteins (EBPs) from P. knowlesi and P. vivax attach to human Duffy antigen receptor for chemokines (DARC) via their Duffy binding-like domains (Pv-DBL and Pk-DBL respectively) for invasion. Here, we provide a comprehensive overview that presents new insights on the atomic resolution interactions that underpin the binding of human DARC with Pk/Pv-DBLs. Based on extensive structural and biochemical data, we provide a novel, testable and overarching interaction model that rationalizes even contradictory pieces of evidence that have so far existed in the literature on Pk/Pv-DBL/DARC binding determinants. We address the conundrum of how parasite-encoded Pk/Pv-DBLs recognize human DARC via its two sulfated tyrosine residues. We collate evidence for two distinct DARC integration sites on Pk/Pv-DBLs that together likely engage the DARCs sulfated extracellular domain. These analyses are important for both malaria vaccine and inhibitor development efforts that are targeted at abrogating Pk/Pv-DBL/DARC coupling as one avenue to prevent invasion of P. vivax into human red blood cells.

microbiology↗

bioRxiv2017

Warm and wet: robust lipase-producing bacteria from the indoor environment

Lipases are key biocatalysts with important biotechnological applications. With the aim of isolating robust lipolytic microbial strains, we have analyzed the bacterial communities inhabiting two domestic extreme environments: a thermophilic sauna and a dishwasher filter. Scanning electron microscopy revealed biofilm-forming and scattered microorganisms in the sauna and dishwasher sample, respectively. A culture-independent approach based on 16S rRNA analysis indicated a high abundance of Proteobacteria in the sauna sample; and, a large amount of Proteobacteria, Firmicutes, Cyanobacteria and Actinobacteria in the dishwasher filter. With a culture-dependent approach, we isolated 48 bacterial strains, screened their lipolytic activities on media with tributyrin as the main carbon source, and finally selected five isolates for further characterization. These strains, all of them identified as members of the genus Bacillus, displayed optimum lipolytic peaks at pH 6.5 and with 1-2% NaCl, and the activity proved very robust at a wide range of pH (up to 11.5) and added NaCl concentrations (up to 4%). The thermal, pH and salt robustness of the selected isolates is a valuable attribute for these strains, which are promising as highly tolerant biodetergents. To our knowledge, this is the first report regarding the isolation from an indoor environment of Bacillus strains with a high potential for industry.

microbiology↗

bioRxiv2017

The rumen microbiome: an underexplored resource for novel antimicrobial discovery

Antimicrobial peptides (AMPs) are promising drug candidates to target multi-drug resistant bacteria. The rumen microbiome presents an underexplored resource for the discovery of novel microbial enzymes and metabolites, including AMPs. Using functional screening and computational approaches, we identified 181 potentially novel AMPs from a rumen bacterial metagenome. Here, we show that three of the selected AMPs (Lynronne-1, 2 and 3) were effective against numerous bacterial pathogens, including methicillin resistant Staphylococcus aureus (MRSA). No decrease in MRSA susceptibility was observed after 25 days of sub-lethal exposure to these AMPs. The AMPs bound preferentially to bacterial membrane lipids and induced membrane permeability leading to cytoplasmic leakage. Topical administration of Lynronne-1 (10% w/v) to a mouse model of MRSA wound infection elicited a significant reduction in bacterial counts, which was comparable to treatment with 2% mupirocin ointment. Our findings indicate that the rumen microbiome may provide viable alternative antimicrobials for future therapeutic application.

microbiology↗

bioRxiv2017

Hammondia hammondi has a developmental program in vitro that mirrors its stringent two host life cycle

Hammondia hammondi is the nearest relative of Toxoplasma gondii, but unlike T. gondii is obligately heteroxenous. We have compared H. hammondi and T. gondii development in vitro and identified multiple H. hammondi-specific growth states. Despite replicating slower than T. gondii, H. hammondi was resistant to pH-induced tissue cyst formation early after excystation. However, in the absence of stress H. hammondi spontaneously converted to a terminally differentiated tissue cyst stage while T. gondii did not. Cultured H. hammondi could infect new host cells for up to 8 days following excystation, and this period was exploited to generate stably transgenic H. hammondi. Coupled with RNAseq analyses, our data clearly show that H. hammondi zoites grow as stringently regulated life stages that are fundamentally distinct from T. gondii tachyzoites and bradyzoites.

microbiology↗

bioRxiv2017

Intercellular communication via the comX-Inducing Peptide (XIP) of Streptococcus mutans

Gram-positive bacteria utilize exported peptides to coordinate genetic and physiological processes required for biofilm formation, stress responses and ecological competitiveness. One example is activation of natural genetic competence by ComR and the comX-inducing peptide (XIP) in Streptococcus mutans. Although the competence pathway can be activated by addition of synthetic XIP in defined medium, the hypothesis that XIP is able to function as an intercellular signal molecule has not been rigorously tested. Co-culture model systems were developed that included a \"sender\" strain that overexpressed the XIP precursor (ComS) and a \"responder\" strain harboring a GFP reporter fusion to a ComR-activated gene (comX) promoter. The ability of the sender strain to provide a signal to activate GFP expression was monitored at the individual cell and population levels using i) planktonic culture systems, ii) cells suspended in an agarose matrix or iii) cells growing in biofilms. XIP was shown to be freely diffusible and XIP signaling between the S. mutans sender and responder strains did not require cell-to-cell contact. The presence of a sucrose-derived exopolysaccharide matrix diminished the efficiency of XIP signaling in biofilms, possibly by affecting spatial distribution of XIP senders and potential responders. Intercellular signaling was greatly impaired in a strain lacking the primary autolysin, AtlA, and was substantially greater when the sender strain underwent lysis. Collectively, these data provide evidence that S. mutans XIP can indeed function as a peptide signal between cells and highlight the importance of studying signaling with endogenously-produced peptide(s) in populations in various environments and physiologic states.\n\nIMPORTANCEThe comX-inducing peptide (XIP) of Streptococcus mutans is a key regulatory element in the activation of genetic competence, which allows cells to take up extracellular DNA. XIP has been found in cell culture fluids and addition of synthetic XIP to physiologically receptive cells can robustly induce competence gene expression. However, there is a lack of consensus as to whether XIP can function as an intercellular communication signal. Here, we show that XIP indeed signals between cells in S. mutans, but that cell lysis may be a critical factor, as opposed to a dedicated secretion/processing system, in allowing for release of XIP into the environment. The results have important implications in the context of the ecology, virulence and evolution of a ubiquitous human pathogen and related organisms.

microbiology↗

bioRxiv2017

Reciprocal control of motility and biofilm formation by the PdhS2 two-component sensor kinase of Agrobacterium tumefaciens

A core regulatory pathway that directs developmental transitions and cellular asymmetries in Agrobacterium tumefaciens involves two overlapping, integrated phosphorelays. One of these phosphorelays putatively includes four histidine sensor kinase homologues, DivJ, PleC, PdhS1, and PdhS2, and two response regulators, DivK and PleD. In several different alphaproteobacteria, this pathway influences a conserved downstream phosphorelay that ultimately controls the phosphorylation state of the CtrA master response regulator. The PdhS2 sensor kinase reciprocally regulates biofilm formation and swimming motility. In the current study the mechanisms by which the A. tumefaciens sensor kinase PdhS2 directs this regulation are delineated. PdhS2 lacking a key residue for phosphatase activity is markedly deficient in proper control of attachment and motility phenotypes, whereas a kinase-deficient PdhS2 mutant is only modestly affected. A genetic interaction between DivK and PdhS2 is revealed, unmasking one of several connections between PdhS2-dependent phenotypes and transcriptional control by CtrA. Epistasis experiments suggest that PdhS2 can function independently of the CckA sensor kinase, the cognate sensor kinase for CtrA which is inhibited by DivK. PdhS2 dynamically localizes to the daughter cell pole in dividing cells. Global expression analysis of the pdhS2 mutant reveals a restricted regulon, functioning through CtrA to separately control motility and regulate levels of the intracellular signal cyclic diguanylate monophosphate (cdGMP), thereby affecting production of adhesive polysaccharides and attachment. We hypothesize that in A. tumefaciens the CtrA regulatory circuit has expanded to include additional inputs through addition of PdhS-type sensor kinases, likely fine-tuning the response of this organism to the soil microenvironment.\n\nIMPORTANCEBacterial developmental processes, such as morphological transformations and behavioral transitions, are tightly regulated. In many alphaproteobacteria cell division and development are coordinated by a specific suite of conserved histidine kinases and their partnered regulatory proteins. Here we describe how the histidine kinase PdhS2 of Agrobacterium tumefaciens regulates complex phenotypes including biofilm formation and motility. PdhS2 genetically interacts with a single-domain response regulator, DivK, and the intracellular signal cyclic diguanylate monophosphate. PdhS2 dynamically localizes to the new pole of recently divided cells, contributing to the regulatory processes that dictate whether these cells remain motile or initiate biofilm formation. These findings expand our understanding of the complex network that integrates cell division and developmental control in A. tumefaciens and related alphaproteobacteria.

microbiology↗

bioRxiv2017

Gene networks provide a high-resolution view of bacteriophage ecology

Bacteriophages are the most abundant and diverse biological entities on the planet, and new phage genomes are being discovered at a rapid pace from metagenomes. As more novel, uncultured phage genomes are published, new tools are needed for placing these genomes in an ecological and evolutionary context. Phages are difficult to study with phylogenetic methods, because they exchange genes regularly, and no single gene is conserved across all phages. Instead, genome-level networks have been used to group similar viruses into clusters for taxonomy. Here, we show that gene-level networks provide a high-resolution view of phage genetic diversity and offer a novel perspective on virus ecology. To that end, we developed a method that identifies informative associations between a phages annotated host and clusters of genes in the network. Given these associations, we were able to predict a phages host with 86% accuracy at the genus level, while also identifying genes that underlie these virus-host interactions. This approach, thus, provides one of the most accurate means of host prediction while also pointing to directions for future empirical work.

microbiology↗

bioRxiv2017

Reduced chlorhexidine and daptomycin susceptibility arises in vancomycin-resistant Enterococcus faecium after serial chlorhexidine exposure

Vancomycin-resistant Enterococcus faecium (VREfm) are critical public health concerns because they are among the leading causes of hospital-acquired bloodstream infections. Chlorhexidine (CHX) is a bisbiguanide cationic antiseptic that is routinely used for patient bathing and other infection control practices. VREfm are likely frequently exposed to CHX; however, the long-term effects of CHX exposure have not been studied in enterococci. In this study, we serially exposed VREfm to increasing concentrations of CHX for a period of 21 days in two independent experimental evolution trials. Reduced CHX susceptibility emerged (4-fold shift in CHX MIC). Sub-populations with reduced daptomycin (DAP) susceptibility were detected, which were further analyzed by genome sequencing and lipidomic analysis. Across the trials, we identified adaptive changes in genes with predicted or experimentally confirmed roles in chlorhexidine susceptibility (efrE), global nutritional stress response (relA), nucleotide metabolism (cmk), phosphate acquisition (phoU), and glycolipid biosynthesis (bgsB), among others. Moreover, significant alterations in membrane phospholipids were identified. Our results are clinically significant because they identify a link between serial sub-inhibitory CHX exposure and reduced DAP susceptibility. In addition, the CHX-induced genetic and lipidomic changes described in this study offer new insights into the mechanisms underlying the emergence of antibiotic resistance in VREfm.

microbiology↗

bioRxiv2017

Epistasis mediated alleviation of the cost of antibiotic resistance for MRSA

Understanding how multi-drug resistant pathogens evolve is key to identifying means of curtailing their further emergence and dissemination. Fitness costs imposed on bacteria by resistance mechanisms are believed to hamper their dissemination in an antibiotic free environment, however, some have been reported to have little or no cost, which suggests there are few barriers preventing their global spread. One such apparently cost-free resistance mechanism acquired by the major human pathogen Staphylococcus aureus is to the clinically important antibiotic mupirocin, which is mediated by mutation of the highly-conserved and essential isoleucyl-tRNA synthethase (ileS) gene. In Genome Wide Association Studies (GWAS) on two genetically and geographically distinct MRSA lineages we have found this mutation to be associated with changes in bacterial virulence, driven through epistatic interactions with other loci. Given the potential dual effect of this mutation on both antibiotic resistance and virulence we adopted a proteomic approach and observed pleiotropic effects. This analysis revealed that the activity of the secretory apparatus of the PSM family of cytolytic toxins, the Pmt system, is affected in the mupirocin resistant mutant, which explains why it is less toxic. As an energetically costly activity, this reduction in toxicity masks the fitness costs associated with this resistance mutation, a cost that becomes apparent when toxin production is required. Given the widespread use of this antibiotic, and that this resistance often results from a single nucleotide substitution in the ileS gene, these hidden fitness costs provide an explanation for why this resistance mechanism is not more prevalent. This work also demonstrates how population-based genomic analysis of virulence and antibiotic resistance can contribute to uncovering hidden features of the biology of microbial pathogens.

microbiology↗

bioRxiv2017

Characterization of polymorphisms in Plasmodium falciparum artemisinin resistance marker kelch13 in asymptomatic infections in a rural area of Cameroon

BackgroundThe genetic variability of the artemisinin resistance (AR) molecular marker kelch13 has been extensively investigated in Plasmodium falciparum malaria parasites from symptomatic infections in South East (SE) Asia where AR is highly prevalent, as well as in Africa where evidence of AR has emerged only recently. However, molecular surveillance and risk of transmission of AR also require monitoring asymptomatic infection. Here, molecular analyses were used to investigate polymorphisms in kelch13 and their potential for transmission in asymptomatic adults in Bolifamba, Cameroon in Central Africa.\n\nMethodsUsing polymerase chain reaction (PCR), we amplified and sequenced the full length of kelch13 from P. falciparum infections detected in the blood of 33 asymptomatic adults (age: 18-55 years-old) collected in a cross-sectional study from July 2008 to October 2009. Risk of increased transmission was assessed by quantifying gametocytes by qPCR. Quantitative ELISA was used to detect plasma levels of PfHRP2 to establish total parasite burdens associated with asymptomatic infection.\n\nResultsOut of 33 isolates tested, 14 (42.4%) presented at least a single nucleotide polymorphism (SNP) in kelch13. Five non-synonymous SNPs were detected (K189T/N, N217H, R393K and E433K). None were located in the beta-propeller domain, where AR mutations have been detected in both SE Asian and, more recently, African parasites. K189T/N and N217H have been previously reported in African strains, but R393K and E433K are new polymorphisms. Gametocytes were detected in 24.2% of infections, without a significant association with detected Kelch13 polymorphisms. Notably, polymorphisms detected in kelch13 were associated with a significant increase of PfHRP2 plasma levels.\n\nConclusionsThis study provides the baseline prevalence of kelch13 polymorphisms in asymptomatic infection for molecular surveillance in tracking AR, and suggests the need for additional studies to explore the association of kelch13 polymorphisms with P. falciparum burden independent of AR, in this region of Cameroon.

microbiology↗

bioRxiv2017

Multiuse patient monitoring equipment as a risk factor for acquisition of Candida auris

Introduction Introduction Methods Results Discussion References Candida auris is an emerging and multi-drug resistant pathogen recently associated with outbreaks worldwide, often in intensive care settings (1). Following the alerts issued by the CDC and PHE in June 2016 (2,3), a look back exercise in the neurological intensive care unit (NITU) in the Oxford University Hospitals NHS Foundation Trust identified five clinical cases of C. auris infection. After the identification of an additional isolate in a urine sample, a patient and environmental screening programme was introduced in the last week of October 2016. We report here a summary of our initial findings which other affected units may wish to consider as part of their infection prevention and control measures. ...

microbiology↗

bioRxiv2017

A Growing Microcolony can Survive and Support Persistent Propagation of Virulent Phages

Bacteria form colonies and secrete extracellular polymeric substances that surround the individual cells. These spatial structures are often associated with collaboration and quorum sensing between the bacteria. Here we investigate the mutual protection provided by spherical growth of a monoclonal colony during exposure to phages that proliferate on its surface. As a proof of concept we exposed growing colonies of Escherichia coli to a virulent mutant of phage P1. When the colony consists of less than ~ 50000 members it is eliminated, while larger initial colonies allow long-term survival because the growth of bacteria throughout the spherical colony exceeds the killing of bacteria on the surface. A mathematical model pinpoints how this critical colony size depends on key parameters in the phage infection cycle. Surprisingly, we predict that a higher phage adsorption rate would allow substantially smaller colonies to survive a virulent phage.\n\nSignificance StatementBacteria are repeatedly exposed to an excess of phages, and carry evidence of this in terms of multiple defense mechanisms encoded in their genome. In addition to molecular mechanisms, bacteria may exploit the defense of spatial refuges. Here we demonstrate how bacteria can limit the impact of a virulent phage attack by growing as a colony which only exposes its surface to phages. We identify a critical size of the initial colony, below which the phages entirely eliminates the colony, and above which the colony continues to grow despite the presence of phages. Our study suggests that coexistence of phages and bacteria is strongly influenced by the spatial composition of microcolonies of susceptible bacteria.

microbiology↗

bioRxiv2017

Unusual Sulfur Requirements During Laboratory Growth of Leutibacter

Many terrestrial bacteria are assumed to utilize sulfate transport and metabolism as a means for fulfilling cellular sulfur requirements. As such, many defined minimal media for bacterial growth under laboratory conditions contain sulfate as their sulfur source. Herein, an exception to this assumption is described as sulfate transport capabilities have been lost at least once in a lineage of Luteibacter associated with plants and fungi. However, a representative of this lineage (an endohyphal species, Luteibacter sp. 9143) can grow in minimal media when sulfur is supplemented with organic (cysteine and methionine) or inorganic (thiosulfate) compounds, and when co-cultured with its fungal host. A related strain of Luteibacter (UNC366Tsa5.1, isolated from the rhizosphere of Arabidopsis) potentially possesses more limited sulfur acquisition pathways than Luteibacter sp. 9143. These results highlight the surprising sulfur requirements of Luteibacter, which may be illustrative of close associations between these strains and eukaryotes, as well as a need for caution when inferring auxotrophies in a focal strain based on differential growth in minimal versus rich media.\n\nImportanceSulfate is often used as the sulfur source in minimal media. Here we show that some Luteibacter strains cannot utilize sulfate as a sulfur source, likely due to loss of genes encoding transport proteins. As sulfur requirements for Luteibacter can be met through co-culture with their fungal partner, this knowledge could provide a means to engineer better symbiotic relationships between bacteria and fungi that may be relevant for agriculture. Because growth in minimal media can be restored by supplementation with either cysteine or methionine, and in some cases only methionine, this result highlights how unexpected growth requirements could masquerade as auxotrophy for certain strains and conditions.

microbiology↗