Bacterial Assemblages Research Articles

Bacterial Diversity in House Dust: Characterization of a Core Indoor Microbiome

Our indoor microbiome consists of a wide range of microbial taxa. Whilst many of these microbes are benign, some are beneficial, some harmful, yet our knowledge of the spatial heterogeneity of bacterial assemblages in our residential environment remains limited. To investigate the existence of a common core house dust bacterial microbiome we selected household vacuum dusts, collected through a citizen science approach, from homes across two bioclimatic regions (UK, Oceanic/Maritime and Greece, Mediterranean). Following the extraction of DNA from each dust sample, we targeted the bacterial 16S rRNA gene using Illumina NextSeq sequencing. PERMANOVA analysis of the microbial communities at family level grouped samples within their distinct bioclimatic region and SIMPER analysis at genus level identified the statistically significant taxa responsible for driving diversity between these groups. A “common to all” core house dust microbiome consisted of Acinetobacter, Massalia, Rubellimicrobium, Sphingomonas and Staphylococcus; genera typically associated with human occupancy and common environmental sources. Additionally, a “unique location specific” microbiome was identified, reflective of the bioclimatic region. The Greek dusts indicated a lower average diversity than the UK house dusts, with a high abundance of Rhizobiaceae in the Greek samples. Our study highlights citizen science as a powerful approach to access the indoor residential environment, at scale, and establishes the existence of a “core” house dust microbiome independent of bioclimatic region.

Microplastic-associated pathogens and antimicrobial resistance in environment

The ubiquitous use of microplastics and their release into the environment especially the water bodies by anthropogenic/industrial activities are the major resources for microplastic contamination. The widespread and often injudicious use of antimicrobial drugs or antibiotics in various sectors including human health and hygiene, agriculture, animal husbandry and food industries are leading to the release of antibiotics into the wastewater/sewage and other water bodies, particularly in urban setups and thus leads to the antimicrobial resistance (AMR) in the microbes. Microplastics are emerging as the hubs as well as effective carriers of these microbial pathogens beside their AMR-genes (ARGs) in marine, freshwater, sewage/wastewater, and urban river ecosystems. These drug resistant bacteria interact with microplastics forming synthetic plastispheres, the ideal niche for biofilm formations which in turn facilitates the transfer of ARGs via horizontal gene transfer and further escalates the occurrence and levels of AMR. Microplastic-associated AMR is an emerging threat for human health and healthcare besides being a challenge for the research community for effective management/address of this menace. In this review, we encompass the increasing prevalence of microplastics in environment, emphasizing mainly on water environments, how they act as centers and vectors of microbial pathogens with their associated bacterial assemblage compositions and ultimately lead to AMR. It further discusses the mechanistic insights on how microplastics act as hosts of biofilms (creating the plastisphere). We have also presented the modern toolbox used for microplastic-biofilm analyses. A review on potential strategies for addressing microplastic-associated AMR is given with recent success stories, challenges and future prospects.

Anthropogenic activities and seasonal properties jointly drive the assemblage of bacterial communities in subtropical river basins

Anthropogenic activities have inevitably impacted riverine ecosystems, yet their overall contribution to the assemblage of bacterial communities at a large river basin scale remains unclear. In this study, 16S amplicon sequencing was implemented to investigate the bacterial ecosystems in paired water and sediment of North River and West River basins in South China., which contains various anthropogenic environments (e.g., rural/urban area, mining area and livestock area). Subsequently, the links between bacterial community and various types of emerging pollutants in river water were analyzed. The results show that the bacterial assemblage of water and sediment had their own properties that the bacterial community of sediment were mainly affected by seasonal properties, while the bacterial community of water were affected by both seasons and anthropogenic activities. Therein, the aquatic bacterial compositions and abundances were driven by changes in temperature, dissolved oxygen and the emerging pollutants. The dominant phyla Proteobacteria and Firmicutes exhibited adaptability to the mining-affected regions, therein many clades (e.g., Beijerinckiaceae, Acetobacteraceae and Mycobacteriaceae) were also prevalent in the livestock-affected and densely-populated regions. In addition, these two phyla presented associations to the antibiotic resistance in water. The levels of antibiotics, relative antibiotic resistance gens (ARGs) and non-antibiotic pharmaceuticals (NAPs) were closely related to bacterial community composition, diversity and functional diversity, indicating their drive in shifting bacterial communities. Collectively, this work provides a basis for understanding the contribution of anthropogenic activities in shifting bacterial community at a large river basin scale. Further, the results provide new insights for expansion of ecological assessment.

Unexpected associations between respiratory viruses and bacteria with Pulmonary Function Testing in children suffering from Cystic Fibrosis (MUCOVIB study)

BackgroundVarious bacterial and viral assemblages composing Cystic Fibrosis (CF) lung microbiota contribute to long-term lung function decline over time. Yet, the impact of individual microorganisms on pulmonary functions remains uncertain in children with CF. MethodsAs part of the ‘Mucoviscidosis, respiratory VIruses, intracellular Bacteria and fastidious organisms’’ project, children with CF were longitudinally followed in a Swiss multicentric study. Respiratory samples included mainly throat swabs and sputa samples for bacterial culture and 16S rRNA metagenomics and nasopharyngeal swabs for respiratory virus detection by molecular assays. Percentage of predicted Forced Expiratory Volume in one second (FEV1%) and Lung Clearance Index (LCI) were recorded. ResultsSixty-one children, of whom 20 (32.8%) presented with at least one pulmonary exacerbation, were included. Almost half of the 363 nasopharyngeal swabs tested by RT-PCR were positive for a respiratory virus, mainly rhinovirus (26.5%). From linear mixed-effects regression models, P. aeruginosa (-11.35, 95%CI [-17.90; -4.80], p = 0.001) was significantly associated with a decreased FEV1%, whereas rhinovirus was associated with a significantly higher FEV1% (+4.24 95%CI [1.67; 6.81], p = 0.001). Compared to conventional culture, 16S rRNA metagenomics showed a sensitivity and specificity of 80.0% and 85.4%, respectively for detection of typical CF pathogens. However, metagenomics detected a bacteria almost twice more often than culture. ConclusionsAs expected, P. aeruginosa impacted negatively on FEV1% while rhinovirus was surprisingly associated with better FEV1%. Culture-free assays identifie significantly more pathogens than standard culture, with disputable clinical correlation.

Highly Variable and Non-complex Diazotroph Communities in Corals From Ambient and High CO2 Environments

The ecological success of corals depends on their association with microalgae and a diverse bacterial assemblage. Ocean acidification (OA), among other stressors, threatens to impair host-microbial metabolic interactions that underlie coral holobiont functioning. Volcanic CO2 seeps offer a unique opportunity to study the effects of OA in natural reef settings and provide insight into the long-term adaptations under a low pH environment. Here we compared nitrogen-fixing bacteria (diazotrophs) associated with four coral species (Pocillopora damicornis, Galaxea fascicularis, Acropora secale, and Porites rus) collected from CO2 seeps at Tutum Bay (Papua New Guinea) with those from a nearby ambient CO2 site using nifH amplicon sequencing to characterize the effects of seawater pH on bacterial communities and nitrogen cycling. Diazotroph communities were of generally low diversity across all coral species and for both sampling sites. Out of a total of 25 identified diazotroph taxa, 14 were associated with P. damicornis, of which 9 were shared across coral species. None of the diazotroph taxa, however, were consistently found across all coral species or across all samples within a species pointing to a high degree of diazotroph community variability. Rather, the majority of sampled colonies were dominated by one or two diazotroph taxa of high relative abundance. Pocillopora damicornis and Galaxea fascicularis that were sampled in both environments showed contrasting community assemblages between sites. In P. damicornis, Gammaproteobacteria and Cyanobacteria were prevalent under ambient pCO2, while a single member of the family Rhodobacteraceae was present at high relative abundance at the high pCO2 site. Conversely, in G. fascicularis diazotroph communities were indifferent between both sites. Diazotroph community changes in response to OA seem thus variable within as well as between host species, potentially arguing for haphazard diazotroph community assembly. This warrants further research into the underlying factors structuring diazotroph community assemblages and their functional role in the coral holobiont.

Influence of aphotic haloclines and euxinia on organic biomarkers and microbial communities in a thalassohaline and alkaline volcanic crater lake.

Studies on microbial communities, and their associated organic biomarkers, that are found thriving in the aphotic euxinic waters in modern stratified ecosystems are scarce compared to those undertaken in euxinic photic zones. The Dziani Dzaha (Mayotte, Indian Ocean) is a tropical, saline, alkaline crater lake that has recently been presented as a modern analog of Proterozoic Oceans due to its thalassohaline classification (having water of marine origin) and specific biogeochemical characteristics. Continuous intense photosynthetic production and microbial mineralization keep most of the water column permanently aphotic and anoxic preventing the development of a euxinic (sulfidic and anoxic) photic zone despite a high sulfide/sulfate ratio and the presence of permanent or seasonal haloclines. In this study, the molecular composition of the organic matter in Lake Dziani Dzaha was investigated and compared to the microbial diversity evaluated through 16S rRNA gene amplicon sequencing, over two contrasting seasons (rainy vs. dry) that influence water column stratification. Depth profiles of organic biomarker concentrations (chlorophyll-a and lipid biomarkers) and bacterial and archaeal OTU abundances appeared to be strongly dependent on the presence of aphotic haloclines and euxinia. OTU abundances revealed the importance of specific haloalkaliphilic bacterial and archaeal assemblages in phytoplanktonic biomass recycling and the biogeochemical functioning of the lake, suggesting new haloalkaline non-phototrophic anaerobic microbial precursors for some of the lipid biomarkers. Uncultured Firmicutes from the family Syntrophomonadaceae (Clostridiales), and Bacteroidetes from the ML635J-40 aquatic group, emerged as abundant chemotrophic bacterial members in the anoxic or euxinic waters and were probably responsible for the production of short-chain n-alkenes, wax esters, diplopterol, and tetrahymanol. Halocline-dependent euxinia also had a strong impact on the archaeal community which was dominated by Woesearchaeota in the sulfide-free waters. In the euxinic waters, methanogenic Euryarchaeota from the Methanomicrobia, Thermoplasmata, and WSA2classes dominated and were likely at the origin of common hydrocarbon biomarkers of methanogens (phytane, pentamethyl-eicosenes, and partially hydrogenated squalene).

Habitat Disturbance Linked with Host Microbiome Dispersion and Bd Dynamics in Temperate Amphibians.

Anthropogenic habitat disturbances can dramatically alter ecological community interactions, including host-pathogen dynamics. Recent work has highlighted the potential for habitat disturbances to alter host-associated microbial communities, but the associations between anthropogenic disturbance, host microbiomes, and pathogens are unresolved. Amphibian skin microbial communities are particularly responsive to factors like temperature, physiochemistry, pathogen infection, and environmental microbial reservoirs. Through a field survey on wild populations of Acris crepitans (Hylidae) and Lithobates catesbeianus (Ranidae), we assessed the effects of habitat disturbance and connectivity on environmental bacterial reservoirs, Batrachochytrium dendrobatidis (Bd) infection, and skin microbiome composition. We found higher measures of microbiome dispersion (a measure of community variability) in A. crepitans from more disturbed ponds, supporting the hypothesis that disturbance increases stochasticity in biological communities. We also found that habitat disturbance limited microbiome similarity between locations for both species, suggesting greater isolation of bacterial assemblages in more disturbed areas. Higher disturbance was associated with lower Bd prevalence for A. crepitans, which could signify suboptimal microclimates for Bd in disturbed habitats. Combined, our findings show that reduced microbiome stability stemming from habitat disturbance could compromise population health, even in the absence of pathogenic infection.

Soil salinity and nutrients availability drive patterns in bacterial community and diversity along succession gradient in the Yellow River Delta

Exploring the main driving factors of microbial community in different succession stages of coastal wetland could provide insights into ecological restoration activities. The present study examined the soil microbial assemblage in a succession gradient of the coastal wetland in the Yellow River Delta (YRD) and elucidated the contributions of spatial structure, vegetation, and soil properties to microbial communities. Plant and soil samples in four succession stages from (S1, S2, S3, and S4) were selected in the coastal wetland of YRD. Soil bacterial community was analyzed using the 16S rRNA high-throughput sequencing technique. Partial mantel test and redundancy analysis were conducted to elucidate the relationship between bacterial community structure and environmental parameters. Soil pH and salinity decreased and soil nutrients increased with succession from mud flat to the late stage. Higher bacterial richness and diversity were also observed with coastal wetland succession. Although most of the soil properties, vegetation, and spatial distribution have an impact on the bacterial community, soil salinity and nutrient availability (e.g., total nitrogen content, nitrate content and dissolved organic carbon) have the greatest influence on the shift in the bacterial community along the succession gradient. Taken together, soil salinity and nutrients availability could be major drivers of variations in bacterial assemblage with coastal wetland succession. These findings improve our understanding of soil microbes as affected by environmental factors and microbial diversity could be considered as a helpful tool to evaluate the efficiency of ecological restoration in coastal wetlands.

Fate of glacier surface snow-originating bacteria in the glacier-fed hydrologic continuums.

Glaciers represent important biomes of Earth and are recognized as key species pools for downstream aquatic environments. Worldwide, rapidly receding glaciers are driving shifts in hydrology, species distributions and threatening microbial diversity in glacier-fed aquatic ecosystems. However, the impact of glacier surface snow-originating taxa on the microbial diversity in downstream aquatic environments has been little explored. To elucidate the contribution of glacier surface snow-originating taxa to bacterial diversity in downstream aquatic environments, we collected samples from glacier surface snows, downstream streams and lakes along three glacier-fed hydrologic continuums on the Tibetan Plateau. Our results showed that glacier stream acts as recipients and vectors of bacteria originating from the glacier environments. The contributions of glacier surface snow-originating taxa to downstream bacterial communities decrease from the streams to lakes, which was consistently observed in three geographically separated glacier-fed ecosystems. Our results also revealed that some rare snow-originating bacteria can thrive along the hydrologic continuums and become dominant in downstream habitats. Finally, our results indicated that the dispersal patterns of bacterial communities are largely determined by mass effects and increasingly subjected to local sorting of species along the glacier-fed hydrologic continuums. Collectively, this study provides insights into the fate of bacterial assemblages in glacier surface snow following snow melt and how bacterial communities in aquatic environments are affected by the influx of glacier snow-originating bacteria.

Arbuscular mycorrhizal fungi and nitrilotriacetic acid regulated Suaeda salsa growth in Cd-contaminated saline soil by driving rhizosphere bacterial assemblages

Phytoremediation is an environmentally friendly method to remediate heavy metal contaminated saline soil. Arbuscular mycorrhizal fungi (AMF) and biodegradable chelators have potential roles in enhancing the phytoremediation efficiency, while their combined effects are largely unexplored. This study was objected to evaluate the effects of AMF and nitrilotriacetic acid (NTA) on phytoremediation using Suaeda salsa. A pot experiment consisting of four treatments (CK, AMF, NTA and AMF + NTA) was conducted for this purpose. The results showed that the shoot and root biomass of Suaeda salsa ranged from 1.84 to 5.86 mg kg−1 and 0.09 to 0.48 mg kg−1 respectively, and were the highest in the AMF + NTA treatment. The AMF + NTA treatment enhanced the Na accumulation by 116 % and 490 %, and enhanced Cd accumulation by 61 % and 33 %, respectively, in plant shoots and roots compared with the CK. The AMF treatment significantly promoted the dominance of Actinobacteria (mainly including Arenimonas, Gaiella, Nocardioides and Marmoricola), whereas the AMF + NTA treatment enhanced that of Proteobacteria (mainly including Aminobacter, Candidatus_Paracaedibacter, Longimicrobium and Flavitalea) in rhizosphere bacterial communities. Network analysis revealed that the bacteria related to Cd were independent from that related to Na in the AMF treatment, but they were consistent in the AMF + NTA treatment. Structural equation modeling further confirmed that single application of AMF or NTA affected plant growth both directly and indirectly, and their combined application could further promote phytoremediation efficiency by enhancing the interactions among bacteria, soil and plants. This study not only proved the benefit of the combined application of AMF and NTA to the improvement of phytoremediation efficiency, but also provided insights into the mechanisms for the improvement from the perspective of rhizosphere microbial community changes.

Mangrove microbiota along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America): Drivers and potential bioindicators

The microbial communities inhabiting the Atlantic-East Pacific (AEP) mangroves have been poorly studied, and mostly comprise chronically polluted mangroves. In this study, we characterized changes in the structure and diversity of microbial communities of mangroves along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America) that experience low human impact. The microbial communities were assigned into 50 phyla. Proteobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, and Planctomycetes were the most abundant taxa. The environmental determinants found to significantly correlated to the microbial communities at these mangroves were granulometry, dieldrin concentration, pH, and total carbon (TC) content. Furthermore, a precise analysis of the sediment highlights the existence of three types of anthropogenic pressure among the stations: (i) organic matter (OM) enrichment due to the proximity to the city and its wastewater treatment plant, (ii) dieldrin contamination, and (iii) naphthalene contamination. These forms of weak anthropogenic pressure seemed to impact the bacterial population size and microbial assemblages. A decrease in Bathyarchaeota, “Candidatus Nitrosopumilus”, and Nitrospira genera was observed in mangroves subjected to OM enrichment. Mangroves polluted with organic contaminants were enriched in Desulfobacteraceae, Desulfarculaceae, and Acanthopleuribacteraceae (with dieldrin or polychlorobiphenyl contamination), and Chitinophagaceae and Geobacteraceae (with naphthalene contamination). These findings provide insights into the main environmental factors shaping microbial communities of mangroves in the AEP that experience low human impact and allow for the identification of several potential microbial bioindicators of weak anthropogenic pressure.

Antibiotics and temperature interact to disrupt soil communities and nutrient cycling

Soils contain immense diversity and support terrestrial ecosystem functions, but they face both anthropogenic and environmental stressors. While many studies have examined the influence of individual stressors on soils, how these perturbations will interact to shape soil communities and their ability to cycle nutrients is far less resolved. Here, we hypothesized that when soils experience multiple stressors their ability to maintain connected and stable communities is disrupted, leading to shifts in C and N pools. To test this, we maintained soils across three temperatures representative of seasonal variability (15, 20 and 30 °C) and introduced high or low doses of the common livestock antibiotic Monensin. We monitored respiration and examined changes to microbial communities through amplicon sequencing and network analyses. We also examined soil C and N pools to understand how temperature and antibiotics shape ecosystem function. We found that antibiotics and rising soil temperatures interacted to disrupt bacterial assemblages and network structure, allowing for a rise in fungal dominance and change in soil nutrient stoichiometry. Antibiotics alone decreased bacterial diversity, abundance, total extractable N, and microbial carbon use efficiency, while increasing bioavailable C. Higher temperatures independently homogenized fungal community composition, decreased dissolved organic C and increased soil respiration rates. These results emphasize that as soils encounter multiple stressors, ecosystem efficiency, stability and resilience may be diminished.

Microbes on decomposing litter in streams: entering on the leaf or colonizing in the water?

When leaves fall in rivers, microbial decomposition commences within hours. Microbial assemblages comprising hundreds of species of fungi and bacteria can vary with stream conditions, leaf litter species, and decomposition stage. In terrestrial ecosystems, fungi and bacteria that enter soils with dead leaves often play prominent roles in decomposition, but their role in aquatic decomposition is less known. Here, we test whether fungi and bacteria that enter streams on senesced leaves are growing during decomposition and compare their abundances and growth to bacteria and fungi that colonize leaves in the water. We employ quantitative stable isotope probing to identify growing microbes across four leaf litter species and two decomposition times. We find that most of the growing fungal species on decomposing leaves enter the water with the leaf, whereas most growing bacteria colonize from the water column. Results indicate that the majority of bacteria found on litter are growing, whereas the majority of fungi are dormant. Both bacterial and fungal assemblages differed with leaf type on the dried leaves and throughout decomposition. This research demonstrates the importance of fungal species that enter with the leaf on aquatic decomposition and the prominence of bacteria that colonize decomposing leaves in the water.

A fungal powdery mildew pathogen induces extensive local and marginal systemic changes in the Arabidopsis thaliana microbiota.

Powdery mildew is a foliar disease caused by epiphytically growing obligate biotrophic ascomycete fungi. How powdery mildew colonization affects host resident microbial communities locally and systemically remains poorly explored. We performed powdery mildew (Golovinomyces orontii) infection experiments with Arabidopsis thaliana grown in either natural soil or a gnotobiotic system and studied the influence of pathogen invasion into standing natural multi-kingdom or synthetic bacterial communities (SynComs). We found that after infection of soil-grown plants, G. orontii outcompeted numerous resident leaf-associated fungi while fungal community structure in roots remained unaltered. We further detected a significant shift in foliar but not root-associated bacterial communities in this setup. Pre-colonization of germ-free A. thaliana leaves with a bacterial leaf-derived SynCom, followed by G. orontii invasion, induced an overall similar shift in the foliar bacterial microbiota and minor changes in the root-associated bacterial assemblage. However, a standing root-derived SynCom in root samples remained robust against foliar infection with G. orontii. Although pathogen growth was unaffected by the leaf SynCom, fungal infection caused a twofold increase in leaf bacterial load. Our findings indicate that G. orontii infection affects mainly microbial communities in local plant tissue, possibly driven by pathogen-induced changes in source-sink relationships and host immune status.

Agricultural Fast Food: Bats Feeding in Banana Monocultures Are Heavier but Have Less Diverse Gut Microbiota

Habitat alteration for agriculture can negatively affect wildlife physiology and health by decreasing diet diversity and increasing exposure to agrochemicals for animals foraging in altered landscapes. Such negative effects may be mediated by the disruption of the gut microbiota (termed dysbiosis), yet evidence for associations between habitat alteration, wildlife health, and the gut microbiota remains scarce. We examine the association between management intensity of banana plantations and both the body condition and gut microbiota composition of nectar-feeding bats Glossophaga soricina, which commonly forage within banana plantations across Latin America. We captured and measured 196 bats across conventional monocultures, organic plantations, and natural forests in Costa Rica, and quantified gut microbiome bacterial phylogenetic diversity using 16S rRNA amplicon sequencing. We found that gut microbiota from bats foraging in conventional monocultures were overall less phylogenetically diverse than those from bats foraging in organic plantations or natural forests, both of which were characterized by diverse bacterial assemblages and individualized microbiota. Despite lower diversity, co-occurrence network complexity was higher in conventional monocultures, potentially indicating altered microbial interactions in agricultural landscapes. Bats from both organic and conventional plantations tended to be larger and heavier than their forest counterparts, reflecting the higher food supply. Overall, our study reveals that whilst both conventional monocultures and organic plantations provide a reliable food source for bats, conventional monocultures are associated with less diverse and potentially dysbiotic microbiota, whilst organic plantations promote diverse and individualized gut microbiota akin to their natural forest-foraging counterparts. Whilst the long-term negative effects of anthropogenically-altered microbiota are unclear, our study provides further evidence from a novel perspective that organic agricultural practices are beneficial for wildlife health.

The potential role of fertilizer-derived exogenous bacteria on soil bacterial community assemblage and network formation

Manure fertilization contributes to crop production and sustainable agriculture by introducing large amounts of nutrients and exogenous microbes into soil. However, the contribution of exogenous microbes in shaping soil bacterial community and network structure after fertilization are still controversial. In this study, bacterial communities and network structure that received unsterilized (R + C) or sterilized (R + SC) manure fertilizers, as well as no fertilizer control (R), were characterized using high throughput sequencing. Results showed that the relative abundance of fertilizer-derived OTUs decreased from 10.4% to 4.6% after 90 days incubation, while the Bray-Curtis distance between the control and fertilization group (R + C and R + SC) gradually increased with the culture time. It can be supposed that manure fertilization altered soil bacterial communities by interfering the growth of indigenous bacteria rather than the colonization of fertilizer-derived bacteria. Network analysis showed that a subset of the fertilizer-derived OTUs identified as Xanthomonadales order and Promicromonospora, Constrictibacter genera acted as connectors between modules. They enhanced the interactions not only between soil-derived OTUs and fertilizer-derived OTUs, but also within indigenous bacteria, supported that the introduction of fertilizer-derived exogenous bacteria contributes large to soil bacterial network association. Moreover, fertilizer-derived OTUs presented to be positively correlated with soil pH, while majority soil-derived OTUs presented to be negatively correlated with various physicochemical variables (pH, DOC, NO3−, and LAP). Our study highlighted the critical role of fertilizer-derived bacteria in regulating indigenous soil microbial community and network formation after fertilization.

Pathogen Biocontrol Using Plant Growth-Promoting Bacteria (PGPR): Role of Bacterial Diversity.

A vast microbial community inhabits in the rhizosphere, among which, specialized bacteria known as Plant Growth-Promoting Rhizobacteria (PGPR) confer benefits to host plants including growth promotion and disease suppression. PGPR taxa vary in the ways whereby they curtail the negative effects of invading plant pathogens. However, a cumulative or synergistic effect does not always ensue when a bacterial consortium is used. In this review, we reassess the disease-suppressive mechanisms of PGPR and present explanations and illustrations for functional diversity and/or stability among PGPR taxa regarding these mechanisms. We also provide evidence of benefits when PGPR mixtures, rather than individuals, are used for protecting crops from various diseases, and underscore the critical determinant factors for successful use of PGPR mixtures. Then, we evaluate the challenges of and limitations to achieving the desired outcomes from strain/species-rich bacterial assemblages, particularly in relation to their role for plant disease management. In addition, towards locating additive or synergistic outcomes, we highlight why and how the benefits conferred need to be categorized and quantified when different strains/species of PGPR are used in combinations. Finally, we highlight the critical approaches needed for developing PGPR mixtures with improved efficacy and stability as biocontrols for utilization in agricultural fields.

Effects of organic acids on the chemotaxis profiles and biocontrol traits of antagonistic bacterial endophytes against root-rot disease in Panax notoginseng.

Understanding the role of chemotaxis in ecological interactions between plants and microbes in the rhizosphere is necessary to optimize biocontrol strategies targeting plant soil-borne diseases. Therefore, we examined and profiled the antagonistic endophytic bacteria (AEB) population with chemotaxis potential in the medicinal plant Panax notoginseng using a cheA gene-based approach coupled with 16S rRNA sequencing. Phylogenetic analysis of the chemotactic AEB (CAEB) community in P. notoginseng enabled the identification of 56 CAEB strains affiliated with 30 species of Actinobacteria, Firmicutes, and Proteobacteria; Firmicutes, especially Bacillus, were predominant. We then systematically quantified the chemotactic response profiles of CAEB toward five organic acid (OA) attractants: citric acid, fumaric acid (FA), malic acid, oxalic acid, and succinic acid. Further hierarchical cluster analysis revealed that the chemotaxis of CAEB to the same attractant exhibited different patterns among not only genera but also species and even strains of the same species. Following chemotaxis and hierarchical analysis, we selected the strongest chemoattractant, fumaric acid (FA), as the target for evaluating the effects of OAs on the representative CAEB strain Bacillus amyloliquefaciens subsp. plantarum YP1. Application of FA significantly stimulated the chemotaxis ability and growth of YP1, and increased the transcript levels of cheA and biocontrol-related genes in YP1. This is the first study to characterise the diversity of chemotaxis profiles toward OAs in natural bacterial assemblages of P. notoginseng and to highlight how FA promotes the biocontrol-related traits of P. notoginseng-associated CAEB.

A Tad-like apparatus is required for contact-dependent prey killing in predatory social bacteria.

Myxococcus xanthus, a soil bacterium, predates collectively using motility to invade prey colonies. Prey lysis is mostly thought to rely on secreted factors, cocktails of antibiotics and enzymes, and direct contact with Myxococcus cells. In this study, we show that on surfaces the coupling of A-motility and contact-dependent killing is the central predatory mechanism driving effective prey colony invasion and consumption. At the molecular level, contact-dependent killing involves a newly discovered type IV filament-like machinery (Kil) that both promotes motility arrest and prey cell plasmolysis. In this process, Kil proteins assemble at the predator-prey contact site, suggesting that they allow tight contact with prey cells for their intoxication. Kil-like systems form a new class of Tad-like machineries in predatory bacteria, suggesting a conserved function in predator-prey interactions. This study further reveals a novel cell-cell interaction function for bacterial pili-like assemblages.

BactoTraits – A functional trait database to evaluate how natural and man-induced changes influence the assembly of bacterial communities

In the environment, abiotic (climatic conditions, physico-chemical parameters), biotic (interactions between microorganisms, vegetation and fauna), and anthropogenic (stress, pollution) filters are driving the microbial diversity observed locally. A key question in microbial ecology is to understand the impact of these filters on bacterial diversity and ecosystem functioning. To highlight the responses of bacterial assemblages to these ecological filters, a new approach based on bacterial functional traits has been developed. This approach provides a functional picture of bacterial assemblages using morphological, physiological, and genomic traits as proxies of functions, and leads to a generalizable approach over a larger range of ecosystems with different bacterial diversities.We have created a user-friendly database of bacterial functional traits, thanks to the properties of 19,455 bacterial strains. This database has been called BactoTraits. For example, oxygen preference, size and shape of bacteria, motility, optimum and range of pH and temperature, genome GC percent and trophic type are among the 19 traits included in BactoTraits. Based on the best-informed strains in the database, we identified five functional groups (i.e. mesophiles, competitors, colonizers, stress-sensitives and stress-tolerants) exhibiting a wide strain taxonomic diversity but with quite similar trait profile combinations.As an example of application, BactoTraits was used to characterize the traits and functional diversity of bacterial assemblages in soil samples from 10 sites with different physico-chemical properties and various levels of metal and polycyclic aromatic hydrocarbon (PAH) contaminations. Inference of functional traits was based on taxonomic diversity information obtained by high-throughput sequencing of 16S rDNA. This trait-based approach has allowed to discriminate soils according to their physico-chemical properties and levels of contamination and to go further into the description of the bacterial assemblages. Several bacterial traits were identified as indicators of specific contaminants such as metals (e.g. filament shape, microaerophile and temperature optimum/range higher than 40 °C) or PAHs (e.g. spherical shape, facultative anaerobe/aerobe, no spore production, pH optimum ≥ 8, low temperature optimum but high temperature variation tolerance).Inferring trait values from a taxonomy-based approach can be extended readily to other microbial systems and contexts such as (i) studies on soils and aquatic ecosystems, (ii) microbial ecology along various environmental gradients, (iii) human, plant and animal microbiotes, as well as (iv) trophic interactions between bacterial communities and their predators.