Resident Bacterial Communities Research Articles

Microscale advection governs microbial growth and oxygen consumption in macroporous aggregates.

Most microbial life on Earth is found in localized microenvironments that collectively exert a crucial role in maintaining ecosystem health and influencing global biogeochemical cycles. In many habitats such as biofilms in aquatic systems, bacterial flocs in activated sludge, periphyton mats, or particles sinking in the ocean, these microenvironments experience sporadic or continuous flow. Depending on their microscale structure, pores and channels through the microenvironments permit localized flow that shifts the relative importance of diffusive and advective mass transport. How this flow alters nutrient supply, facilitates waste removal, drives the emergence of different microbial niches, and impacts the overall function of the microenvironments remains unclear. Here, we quantify how pores through microenvironments that permit flow can elevate nutrient supply to the resident bacterial community using a microfluidic experimental system and gain further insights from coupled population-based and computational fluid dynamics simulations. We find that the microscale structure determines the relative contribution of advection vs diffusion, and even a modest flow through a pore in the range of 10 µm s-1 can increase the carrying capacity of a microenvironment by 10%. Recognizing the fundamental role that microbial hotspots play in the Earth system, developing frameworks that predict how their heterogeneous morphology and potential interstitial flows change microbial function and collectively alter global scale fluxes is critical.IMPORTANCEMicrobial life is a key driver of global biogeochemical cycles. Similar to the distribution of humans on Earth, they are often not homogeneously distributed in nature but occur in dense clusters that resemble microbial cities. Within and around these clusters, diffusion is often assumed as the sole mass-transfer process that dictates nutrient supply and waste removal. In many natural and engineered systems such as biofilms in aquatic environments, aggregates in bioremediation, or flocs in wastewater treatment plants, these clusters are exposed to flow that elevates mass transfer, a process that is often overlooked. In this study, we show that advective fluxes can increase the local growth of bacteria in a single microenvironment by up to 50% and shape their metabolism by disrupting localized anoxia or supplying nutrients at different rates. Collectively, advection-enhanced mass transport may thus regulate important biogeochemical transformations in both natural and engineered environments.

Site properties, environmental factors, and crop identify influence soil bacterial communities more than municipal biosolid application

Reducing the environmental impact of Canadian field crop agriculture, including the reliance on conventional synthesised fertilisers, are key societal targets for establishing long-term sustainable practices. Municipal biosolids (MSB) are an abundant, residual organic material, rich in phosphate, nitrogen and other oligo-nutrients, that could be used in conjunction with conventional fertilisers to decrease their use. Though MBS have previously been shown to be an effective fertiliser substitute for different crops, including corn and soybean, there remain key knowledge gaps concerning the impact of MBS on the resident soil bacterial communities in agro-ecosystems. We hypothesised that the MBS fertiliser amendment would not significantly impact the structure or function of the soil bacterial communities, nor contribute to the spread of human pathogenic bacteria, in corn or soybean agricultural systems. In field experiments, fertiliser regimes for both crops were amended with MBS, and compared to corn and soybean plots with standard fertiliser treatments. We repeated this across four different agricultural sites in Quebec, over 2021 and 2022. We sampled MBS-treated, and untreated soils, and identified the composition of the soil bacterial communities via 16S rRNA metabarcoding. We found no indication that the MBS fertiliser amendment altered the structure of the soil bacterial communities, but rather that the soil type and crop identities were the most significant factors in structuring the bacterial communities. Moreover, there was no evidence that the MBS-treated soils were enriched in potential human bacterial pathogens over the two years of our study. Our analysis indicates that not only can MBS function as substitutes for conventional, synthesised fertilisers, but that they also do not disrupt the structure of the resident soil bacterial communities in the short term. Finally, we suggest that the use of MBS in agro-ecosystems poses no greater concern to the public than existing soil bacterial communities. This highlights the significant role MBS could potentially have in reducing the use of conventional industrial fertilisers and improving agricultural production, without risking environmental contamination.

Survival of a microbial inoculant in soil after recurrent inoculations

Microbial inoculants are attracting growing interest in agriculture, but their efficacy remains unreliable in relation to their poor survival, partly due to the competition with the soil resident community. We hypothesised that recurrent inoculation could gradually alleviate this competition and improve the survival of the inoculant while increasing its impact on the resident bacterial community. We tested the effectiveness of such strategy with four inoculation sequences of Pseudomonas fluorescens strain B177 in soil microcosms with increasing number and frequency of inoculation, compared to a non-inoculated control. Each sequence was carried out at two inoculation densities (106 and 108 cfu.g soil−1). The four-inoculation sequence induced a higher abundance of P. fluorescens, 2 weeks after the last inoculation. No impact of inoculation sequences was observed on the resident community diversity and composition. Differential abundance analysis identified only 28 out of 576 dominants OTUs affected by the high-density inoculum, whatever the inoculation sequence. Recurrent inoculations induced a strong accumulation of nitrate, not explained by the abundance of nitrifying or nitrate-reducing microorganisms. In summary, inoculant density rather than inoculation pattern matters for inoculation effect on the resident bacterial communities, while recurrent inoculation allowed to slightly enhance the survival of the inoculant and strongly increased soil nitrate content.

Pulsed inputs of high molecular weight organic matter shift the mechanisms of substrate utilisation in marine bacterial communities.

Heterotrophic bacteria hydrolyze high molecular weight (HMW) organic matter extracellularly prior to uptake, resulting in diffusive loss of hydrolysis products. An alternative 'selfish' uptake mechanism that minimises this loss has recently been found to be common in the ocean. We investigated how HMW organic matter addition affects these two processing mechanisms in surface and bottom waters at three stations in the North Atlantic Ocean. A pulse of HMW organic matter increased cell numbers, as well as the rate and spectrum of extracellular enzymatic activities at both depths. The effects on selfish uptake were more differentiated: in Gulf Stream surface waters and productive surface waters south of Newfoundland, selfish uptake of structurally simple polysaccharides increased upon HMW organic matter addition. The number of selfish bacteria taking up structurally complex polysaccharides, however, was largely unchanged. In contrast, in the oligotrophic North Atlantic gyre, despite high external hydrolysis rates, the number of selfish bacteria was unchanged, irrespective of polysaccharide structure. In deep bottom waters (> 4000 m), structurally complex substrates were processed only by selfish bacteria. Mechanisms of substrate processing-and the extent to which hydrolysis products are released to the external environment-depend on substrate structural complexity and the resident bacterial community.

The impact of phage treatment on bacterial community structure is minor compared to antibiotics

Phage treatment is suggested as an alternative to antibiotics; however, there is limited knowledge of how phage treatment impacts resident bacterial community structure. When phages induce bacterial lysis, resources become available to the resident community. Therefore, the density of the target bacterium is essential to consider when investigating the effect of phage treatment. This has never been studied. Thus, we invaded microcosms containing a lake-derived community with Flavobacterium columnare strain Fc7 at no, low or high densities, and treated them with either the bacteriophage FCL-2, the antibiotic Penicillin or kept them untreated (3 × 3 factorial design). The communities were sampled over the course of one week, and bacterial community composition and density were examined by 16S rDNA amplicon sequencing and flow cytometry. We show that phage treatment had minor impacts on the resident community when the host F. columnare Fc7 of the phage was present, as it caused no significant differences in bacterial density α- and β-diversity, successional patterns, and community assembly. However, a significant change was observed in community composition when the phage host was absent, mainly driven by a substantial increase in Aquirufa. In contrast, antibiotics induced significant changes in all community characteristics investigated. The most crucial finding was a bloom of γ-proteobacteria and a shift from selection to ecological drift dominating community assembly. This study investigated whether the amount of a bacterial host impacted the effect of phage treatment on community structure. We conclude that phage treatment did not significantly affect the diversity or composition of the bacterial communities when the phage host was present, but introduced changes when the host was absent. In contrast, antibiotic treatment was highly disturbing to community structure. Moreover, higher amounts of the bacterial host of the phage increased the contribution of stochastic community assembly and resulted in a feast-famine like response in bacterial density in all treatment groups. This finding emphasises that the invader density used in bacterial invasion studies impacts the experimental reproducibility. Overall, this study supports that phage treatment is substantially less disturbing to bacterial communities than antibiotic treatments.

Descriptive analyses of bacterial communities in marine sediment microcosms spiked with fish wastes, emamectin benzoate, and oxytetracycline

In marine sediments surrounding salmon aquaculture sites, organic matter (OM) enrichment has been shown to influence resident bacterial community composition; however, additional effects on these communities due to combined use of the sea-lice therapeutant emamectin benzoate (EMB) and the widely used antibiotic oxytetracycline (OTC) are unknown. Here, we use sediment microcosms to assess the influence of OM, EMB, and OTC on benthic bacterial communities. Microcosms consisted of mud or sand sediments enriched with OM (fish and feed wastes) and spiked with EMB and OTC at environmentally-relevant concentrations. Samples were collected from initial matrices at the initiation of the trial and after 110 days for 16 S rRNA gene sequencing of the V3-V4 region and microbiome profiling. The addition of OM in both mud and sand sediments reduced alpha diversities; for example, an average of 1106 amplicon sequence variants (ASVs) were detected in mud with no OM addition, while only 729 and 596 ASVs were detected in mud with low OM and high OM, respectively. Sediments enriched with OM had higher relative abundances of Spirochaetota, Firmicutes, and Bacteroidota. For instance, Spirochaetota were detected in sediments with no OM with a relative abundance range of 0.01–1.2%, while in sediments enriched with OM relative abundance varied from 0.16% to 26.1%. In contrast, the addition of EMB (60 ng/g) or OTC (150 ng/g) did not result in distinct taxonomic shifts in the bacterial communities compared to un-spiked sediments during the timeline of this experiment. EMB and OTC concentrations may have been below effective inhibitor concentrations for taxa in these communities; further work should explore gene content and the presence of antibiotic resistance genes (ARGs) in sediment-dwelling bacteria.

Time from feeding impacts farmed Atlantic salmon (Salmo salar) gut microbiota and faecal score

In intensive Atlantic salmon aquaculture, faecal score potentially serves as a generalised indicator of gut microbiome diversity and composition and as a proxy for gut transit time. There is also the possible application to detect dysbiosis. The utility of using faecal scoring for assessing commercially farmed fish populations may, however, be impacted by rapid temporal changes in digestive status following feeding that, as yet, has not been considered. To help inform sampling strategies and better understand the utility of faecal scoring for farmed fish, this study documented Atlantic salmon faecal scores and gut bacterial 16S rRNA amplicon sequence profiles over 24 h following a feeding event. Samples were collected from two marine cohorts of salmon in different seasons (summer and winter), and comparisons were also made between non-destructive stripped hindgut faeces (HS) and destructive sampling of hindgut digesta (HD) and hind gut mucosa (HM). Average hindgut faecal scores and microbiome diversity were largely consistent over a normal (6 to 8 h) sampling day in winter, but were much more variable in summer, potentially associated with faster faecal passage and dynamic gut microbial changes in the hours after feeding. HS samples were determined to be a valid non-destructive method to obtain material for assessing the diversity and composition of transient bacterial communities in the distal intestine. For an accurate representation of both the transient and resident bacterial communities, both sample types should be considered. It is recommended that studies comparing treatment cohorts, or between individuals in large sample sets, should be designed to capture temporal and seasonal effects that are associated with changes in digestive status and gut microbiome.

Significant antimicrobial-producing vegetation uniquely shapes the stormwater biofilter microbiome with implications for enhanced faecal pathogen inactivation

Biofilters demonstrate promising yet inconsistent removal of faecal pathogens from stormwater. Antimicrobial-producing plants represent safe, inexpensive biofilter design features which can significantly enhance faecal microbe treatment. The microbiota naturally inhabiting biofilters have additionally been established as key mediators of faecal microbe inactivation. To date, however, it remains unknown: (1) to what extent plants, including significant antimicrobial-producing plants, influence the biofilter microbiome; and (2) how this in turn impacts faecal microorganism survival/die-off. The present study employed 16S rRNA sequencing to examine these relationships throughout the soil profiles of differently vegetated biofilters over time. It was found that plants had subtle but significant influences on the composition and structure of resident biofilter bacterial communities, with varying impacts observed throughout biofilter profiles. Bacterial communities inhabiting biofilters comprising significant antimicrobial-producing plants demonstrated distinct compositional and taxonomic differences relative to other configurations. In particular, compared to other biofilters, the best-performing configuration for faecal bacterial treatment, Melaleuca linariifolia (significant antimicrobial-producing plant), exhibited both higher and lower relative frequencies of putative faecal bacterial antagonists (e.g. Actinobacteria) and mutualists (e.g. certain Gammaproteobacteria), respectively. These preliminary findings suggest that antimicrobial plants may enhance populations of microbiota which suppress faecal bacterial survival, and highlight the plant-microbiome relationship as a novel area of focus for optimising biofilter performance.

Cultivar Susceptibility to Olive Knot Disease and Association with Endophytic Microbiota Community

Olive knot disease (OKD) induced by the bacterium Pseudomonas savastanoi pv. savastanoi seriously affects olive production in the Mediterranean basin. Nowadays, the only strategies to control the disease are pruning and the application of cupric products. An essential strategy to enhance protection is represented by the identification of resistant cultivars, which represents a crucial opportunity for future investments and breeding. We undertook a three-year-long survey at the International Olive Germplasm Collection of “Villa Zagaria” (Sicily, Italy) on thirty-six Sicilian cultivars that were monitored for symptom development. Cultivars with different levels of susceptibility were divided into five clusters. Moreover, in order to investigate possible interactions with endophytic microbial communities, two cultivars with contrasting susceptibilities, Zaituna (highly resistant) and Giarraffa (highly susceptible), were selected for an amplicon-based metagenomic analysis. Distinct endophytic communities colonized the two cultivars, suggesting an interaction between the resident bacterial community and the pathogen. Significantly higher bacterial richness was detected in the shoots of the susceptible cv. Giarraffa, although it had lower diversity. The opposite trend was observed for fungal communities. Among the microbes resulted to be enriched in cv. Giarraffa, it is important to underline the presence of Pseudomonas among the bacterial genera, and Alternaria, Neofusicoccum, Epicoccum, Ascochyta, and Elsinoe among the fungal genera, which include many species often described as plant pathogens and biocontrol agents. Starting from this basic information, new strategies of control, which include breeding for resistance and integrated disease management, can be envisaged.

Microbiome in Nasal Mucosa of Children and Adolescents with Allergic Rhinitis: A Systematic Review

The human upper respiratory tract comprises the nasal cavity, pharynx and larynx regions and offers distinct microbial communities. However, an imbalance and alterations in the nasal mucosa microbiome enhance the risk of chronic respiratory conditions in patients with allergic respiratory diseases. This is particularly important in children and adolescents once allergic rhinitis (AR) is an inflammatory disorder of the nasal mucosa, often associated with an increase in pulmonary allergic inflammation. Therefore, this systematic review aimed to collect scientific data published concerning the microbial community alterations in nasal mucosa of children and adolescents suffering from AR or in association with adenotonsillar hypertrophy (AH) and allergic rhinoconjunctivitis (ARC). The current study was performed using the guidelines of Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). Publications related to microbiome alterations in the nasal mucosa in pediatric age, studies including next-generation sequencing platforms, and studies exclusively written in the English language were some of the inclusion criteria. In total, five articles were included. Despite the scarcity of the published data in this research field and the lack of prospective studies, the genera Acinetobacter, Corynebacterium, Dolosigranulum, Haemophilus, Moraxella, Staphylococcus and Streptococcus dominate the nares and nasopharyngeal microbiome of the pediatric population regardless of their age. However, an imbalance in the resident bacterial community in the nasal mucosa was observed. The genera Acinetobacter, and Pseudomonas were more abundant in the nasal cavity of AR and AH children, while Streptococcus and Moraxella were predominant in the hypopharyngeal region of AR infants. An abundance of Staphylococcus spp. was also reported in the anterior nares and hypopharyngeal region of children and adolescents suffering from AR passive smoke exposure and ARC. These records suggest that different nasal structures, ageing, smoke exposure and the presence of other chronic disorders shape the nasal mucosa microbiome. Therefore, the establishment of adequate criteria for sampling would be established for a deeper understanding and a trustworthy comparison of the microbiome alterations in pediatric age.

Changes in Bacterial Communities of Kumamoto Oyster Larvae During Their Early Development and Following Vibrio Infection Resulting in a Mass Mortality Event.

Vibrio and Ostreid herpesvirus 1 are responsible for mass mortalities of oyster larvae in hatcheries. Relevant works have focused on their relationships with the disease when larval mortality occurs. On the contrary, little is known about how the resident microbiota in oyster larvae responds to Vibrio-infected disease causing mortality as the disease progressed, whereas this knowledge is fundamental to unveil the etiology of the disease. Here, we analyzed the temporal succession of the microbiome of Kumamoto oyster (Crassostrea sikamea) larvae during their early development, accompanied by a Vibrio-caused mortality event that occurred at the post D-stage of larval development in a shellfish hatchery in Ningbo, China, on June 2020. The main causative agent of larval mortality was attributable to Vibrio infection, which was confirmed by linearly increased Vibrio abundance over disease progression. Larval bacterial communities dramatically changed over host development and disease progression, as highlighted by reduced α-diversity and less diverse core taxa when the disease occurred. Null model and phylogenetic-based mean nearest taxon distance analyses showed that the relative importance of deterministic processes governing larval bacterial assembly initially increased over host development, whereas this dominance was depleted over disease progression. Furthermore, we screened the disease-discriminatory taxa with a significant change in their relative abundances, which could be indicative of disease progression. In addition, network analysis revealed that disease occurrence remodeled the co-occurrence patterns and niche characteristics of larval microbiota. Our findings demonstrate that the dysbiosis of resident bacterial communities and the shift of microecological mechanisms in the larval microbiome may contribute to mortality during oyster early development.

Interactions between Bacterial Inoculants and Native Soil Bacterial Community: the Case of Spore-forming Bacillus spp.

Microbial diversity can restrict the invasion and impact of alien microbes into soils via resource competition. However, this theory has not been tested on various microbial invaders with different ecological traits, particularly spore-forming bacteria. Here we investigated the survival capacity of two introduced spore-forming bacteria, Bacillus mycoides (BM) and B. pumillus (BP) and their impact on the soil microbiome niches with low and high diversity. We hypothesized that higher soil bacterial diversity would better restrict Bacillus survival via resource competition, and the invasion would alter the resident bacterial communities' niches only if inoculants do not escape competition with the soil community (e.g. through sporulation). Our findings showed that BP could not survive as viable propagules and transiently impacted the bacterial communities' niche structure. This may be linked to its poor resource usage and low growth rate. Having better resource use capacities, BM better survived in soil, though its survival was weakly related to the remaining resources left for them by the soil community. BM strongly affected the community niche structure, ultimately in less diverse communities. These findings show that the inverse diversity-invasibility relationship can be valid for some spore-forming bacteria, but only when they have sufficient resource use capacity.

Microplastics act as a carrier for wastewater-borne pathogenic bacteria in sewage.

Microplastic pollution, a pressing global environmental problem, has a severe impact on both aquatic ecosystems and public health worldwide. Due to the small size of microplastics, they are able to pass through the filtration systems of municipal wastewater treatment works (WWTWs). In recent years, studies have focused on the environmental abundance and ecotoxicological effects of microplastics, but there are limited studies investigating the colonization of microplastics by bacteria, especially those pathogenic ones. In this study, we examined the colonization and composition of the bacterial communities on polyethylene microbeads after incubation in raw sewage collected from three municipal WWTWs in Hong Kong (Sha Tin Sewage Treatment Works, Stonecutters Island Sewage Treatment Works, and Shek Wu Hui Sewage Treatment Works). Scanning electron microscopy (SEM) results indicate that bacterial cells were colonized on the surfaces of the microbeads and formed biofilms after sewage incubation. Metagenomic sequencing data demonstrated an increase in bacterial diversity after 21 days of sewage incubation when compared to shorter incubation periods of 6, 11 and 16 days. Importantly, human and fish pathogens such as Arcobacter cryaerophilus, Aeromonas salmonicida, Vibrio areninigrae and Vibrio navarrensis were found in the resident bacterial communities. Taken together, our results demonstrate that microplastics could act as a carrier for wastewater-borne pathogenic bacteria in municipal sewage.

Comprehensive insights into profiles and bacterial sources of intracellular and extracellular antibiotic resistance genes in groundwater

Antibiotic resistance genes (ARGs), especially last-resort ARGs (LARGs), are receiving extensive attention as emerging environmental contaminants in groundwater. However, their prevalent intracellular and extracellular patterns and bacterial sources in groundwater remain unclear. Herein, groundwater samples were collected in Tianjin, and characterized based on the profiles of intracellular ARGs (iARGs) and extracellular ARGs (eARGs), as well as the resident bacterial communities and extracellular DNA (eDNA)-releasing bacterial communities. The quantitative real-time PCR assays showed that eARGs presented fewer subtypes than iARGs and generally displayed lower detection frequencies than the corresponding iARGs. Similarly, LARGs exhibited lower detection frequencies than common ARGs, but the total abundance showed no significant differences between them. Genes vanA and blaVIM were the observed dominant LARGs, and aadA was the observed common ARG independent of location inside or outside the bacteria. Furthermore, the top 10 phyla showed much difference between the main eDNA-releasing bacteria and the dominant resident bacteria. Proteobacteria was the predominant resident bacterial phyla while dominating the source of eDNA in groundwater. Despite representing a minor portion of the abundance in the resident bacteria, Actinobacteriota, Acidobacteriota, and Chloroflex surprisingly accounted for a large majority of eDNA release. Co-occurrence patterns among persistent ARGs, the resident bacteria, and eDNA-releasing bacteria revealed that the dominant common iARG aadA and intracellular LARGs blaVIM and vanA had significant positive correlations with Methylobacterium_Methylorubrum and Shewanella. Meanwhile, the dominant extracellular LARG blaVIM may be released by bacteria belonging to at least five genera, including Ellin6067, Bifidobacterium, Blautia, Veillonella, and Dechloromonas. Collectively, the findings of this study extend our understanding regarding the distribution of ARGs and their bacterial sources in groundwater, and indicate the serious pollution of LARGs in groundwater, which poses potential risks to public health.

Metagenomic analysis for taxonomic and functional potential of Polyaromatic hydrocarbons (PAHs) and Polychlorinated biphenyl (PCB) degrading bacterial communities in steel industrial soil.

Iron and steel industries are the major contributors to persistent organic pollutants (POPs). The microbial community present at such sites has the potential to remediate these contaminants. The present study highlights the metabolic potential of the resident bacterial community of PAHs and PCB contaminated soil nearby Bhilai steel plant, Chhattisgarh (India). The GC-MS/MS analysis of soil samples MGB-2 (sludge) and MGB-3 (dry soil) resulted in identification of different classes of POPs including PAHs {benzo[a]anthracene (nd; 17.69%), fluorene (15.89%, nd), pyrene (nd; 18.7%), benzo(b)fluoranthene (3.03%, nd), benzo(k)fluoranthene (11.29%; nd), perylene (5.23%; nd)} and PCBs (PCB-15, PCB-95, and PCB-136). Whole-genome metagenomic analysis by Oxford Nanopore GridION Technology revealed predominance of domain bacteria (97.4%; 97.5%) followed by eukaryote (1.4%; 1.5%), archaea (1.2%; 0.9%) and virus (0.02%; 0.04%) in MGB-2 and MGB-3 respectively. Proteobacteria (44.3%; 50.0%) to be the prominent phylum followed by Actinobacteria (22.1%; 19.5%) in MBG-2 and MBG-3, respectively. However, Eukaryota microbial communities showed a predominance of phylum Ascomycota (20.5%; 23.6%), Streptophyta (18.5%, 17.0%) and unclassified (derived from Eukaryota) (12.1%; 12.2%) in MGB-2 and MGB-3. The sample MGB-3 was richer in macronutrients (C, N, P), supporting high microbial diversity than MGB-2. The presence of reads for biphenyl degradation, dioxin degradation, PAH degradation pathways can be further correlated with the presence of PCB and PAH as detected in the MGB-2 and MGB-3 samples. Further, taxonomic vis-à-vis functional analysis identified Burkholderia, Bradyrhizobium, Mycobacterium, and Rhodopseudomonas as the keystone degrader of PAH and PCB. Overall, our results revealed the importance of metagenomic and physicochemical analysis of the contaminated site, which improves the understanding of metabolic potential and adaptation of bacteria growing under POP contaminated environments.

Temporal dynamics of the soil bacterial community following Bacillus invasion

SummaryMicrobial inoculants are constantly introduced into the soil as the deployment of sustainable agricultural practices increases. These introductions might induce soil native communities’ dynamics, influencing their assembly process. We followed the impact and successional trajectories of native soil communities of different diversity levels to the invasion by Bacillus mycoides M2E15 (BM) and B. pumilus ECOB02 (BP). Whereas the impact was more substantial when the invader survived (BM), the transient presence of BP also exerted tangible effects on soil bacterial diversity. Community assembly analyses revealed that deterministic processes primarily drove community turnover. This selection acted stronger in highly diverse communities invaded by BM than in those invaded by BP. We showed that resident bacterial communities exhibit patterns of secondary succession following invasions, even if the latter are unsuccessful. Furthermore, the intensification of biotic interactions in more diverse communities might strengthen the deterministic selection upon invasion in communities with higher diversity.

Organic fertilization regimes suppress fungal plant pathogens through modulating the resident bacterial and protistan communities

AbstractIntroductionFungal plant pathogens are an emerging threat to economically important crop production worldwide and a significant risk to global food security. However, we have limited knowledge of how agricultural management practices drive the emergence and spread of pathogens within crop microbiomes and the underlying ecological mechanisms.Materials and MethodsWe characterized the profiles of potential fungal plant pathogens, as well as bacterial and protistan communities, in sorghum phyllosphere, root endosphere, and rhizosphere and bulk soils collected from a long‐term experiment with multiple inorganic and organic fertilization regimes.ResultsWe found contrasting patterns of fungal plant pathogens across the four sorghum–soil compartments and that organic fertilization regime significantly reduced the diversity and proportions of fungal plant pathogens in rhizosphere and bulk soils. We further found that the changes in fungal plant pathogens were driven more by resident bacterial and protistan communities than by soil physicochemical parameters. There was a significantly negative relationship between the diversity of fungal plant pathogens in the rhizosphere and bulk soils with sorghum yield and protein contents. Structural equation modeling revealed that long‐term organic fertilization regimes contributed to the suppression of fungal plant pathogens mainly through modulating the resident bacterial and protistan communities.ConclusionThese findings advance our understanding of the responses of fungal plant pathogens in crop microbiomes to fertilization regimes, with implications for more targeted strategies to manage the impacts of fungal pathogens on plant health and economic losses.

A new insight into spacing patterns of soil bacterial microbiome induced by root rot of Carya cathayensis

The sustainability of tree crop plantations has become an urgent issue due to the frequent incidence of soil-borne plant diseases. Root rot is a soil-borne disease that can result in severe losses of Carya cathayensis, an economically important plant. However, the disease's transmission characteristics and impact upon the resident bacterial community are poorly known. This study analyzed the microbial communities in bulk and rhizospheric soils over equal geographical distances (4 m) using high-throughput sequencing to explore the transmission pattern and biotic and abiotic driving factors of root rot. The results revealed that available potassium, phosphatase enzyme, and pH were negatively related to root rot incidences. In addition, microbial α-diversity showed opposite variations in bulk and rhizospheric soils but ultimately recovered to the initial healthy levels (P > 0.05), while bacterial structure showed no resilience. In comparison, specific taxa, such as Flavobacterium in bulk soil and Nitrolancea, Microvirga in rhizospheric soil, increased rapidly with rising disease incidences. Besides, rhizospheric communities were involved in a stabler but a less resistant network of disease incidences than bulk soil. This study expands our knowledge of the distance pattern of root rot transmission between plant rhizosphere and soil microorganisms as well as the biotic and abiotic factors driving disease incidences, ultimately offering potential strategies to suppress root rot disease and improve soil health.

Characterization of Bacterial Community Structure Dynamics in a Rat Burn Wound Model Using 16S rRNA Gene Sequencing.

Burns destroy the skin barrier and alter the resident bacterial community, thereby facilitating bacterial infection. To treat a wound infection, it is necessary to understand the changes in the wound bacterial community structure. However, traditional bacterial cultures allow the identification of only readily growing or purposely cultured bacterial species and lack the capacity to detect changes in the bacterial community. In this study, 16S rRNA gene sequencing was used to detect alterations in the bacterial community structure in deep partial-thickness burn wounds on the back of Sprague-Dawley rats. These results were then compared with those obtained from the bacterial culture. Bacterial samples were collected prior to wounding and 1, 7, 14, and 21 days after wounding. The 16S rRNA gene sequence analysis showed that the number of resident bacterial species decreased after the burn. Both resident bacterial richness and diversity, which were significantly reduced after the burn, recovered following wound healing. The dominant resident strains also changed, but the inhibition of bacterial community structure was in a nonvolatile equilibrium state, even in the early stage after healing. Furthermore, the correlation between wound and environmental bacteria increased with the occurrence of burns. Hence, the 16S rRNA gene sequence analysis reflected the bacterial condition of the wounds better than the bacterial culture. 16S rRNA sequencing in the Sprague-Dawley rat burn model can provide more information for the prevention and treatment of burn infections in clinical settings and promote further development in this field.

First characterization of the gut microbiome associated with Mytilus chilensis collected at a mussel farm and from a natural environment in Chile

The gut microbiome of Mytilus chilensis was analyzed using a next-generation sequencing (NGS) approach using as target the V6-V8 16S rDNA gene regions. The resident gut bacterial communities were analyzed in individuals collected from two locations, both free-living in natural conditions (Wild Type group, WT) and those found in intensive commercial cultures at a Mussel Farm (MF group) off the Chilean coast. A total of 1.2 M of non-chimeric sequences were detected, belonging to 30 phyla, including Fusobacteria, Proteobacteria, Bacteroides, Tenericutes, and 404 genera taxa. The major fraction of the sequences detected corresponded to Vibrionaceae and Fusobacteriaceae families for MF and WT groups, respectively. The gut microbiome of M. chilensis showed a wide diversity of microorganisms; however, differences were observed depending on the origin of samples, where gut samples from the mussel farm showed a lower number of genera when compared to gut tissue samples collected from the wild type individuals. The dominant bacterial are Vibrio, Psychrilyobacter, Mycoplasma, and Psychromonas, that were present with different relative abundancies among the samples analyzed. This next generation sequencing technique, applied for the first time in Chilean mussel (M. chilensis), showed that the gut is a useful tissue for the study of bacterial communities in this bivalve mollusk. The results obtained in this work provided insights into the composition of the microbiota of M. chilensis, unravelling the great bacterial diversity and the effect of habitat on the bacterial community structure.