Distinct Bacterial Communities Research Articles

Multiscale Spatial Variability and Stability in the Structure and Diversity of Bacterial Communities Associated with the Kelp Eisenia cokeri in Peru.

Ecological communities are structured by a range of processes that operate over a range of spatial scales. While our understanding of such biodiversity patterns in macro-communities is well studied, our understanding at the microbial level is still lacking. Bacteria can be free living or associated with host eukaryotes, forming part of a wider "microbiome," which is fundamental for host performance and health. For habitat forming foundation-species, host-bacteria relationships likely play disproportionate roles in mediating processes for the wider ecosystem. Here, we describe host-bacteria communities across multiple spatial scales (i.e., from 10s of m to 100s of km) in the understudied kelp, Eisenia cokeri, in Peru. We found that E. cokeri supports a distinct bacterial community compared to the surrounding seawater, but the structure of these communities varied markedly at the regional (~480 km), site (1-10 km), and individual (10s of m) scale. The marked regional-scale differences we observed may be driven by a range of processes, including temperature, upwelling intensity, or regional connectivity patterns. However, despite this variability, we observed consistency in the form of a persistent core community at the genus level. Here, the genera Arenicella, Blastopirellula, Granulosicoccus, and Litorimonas were found in >80% of samples and comprised ~53% of total sample abundance. These genera have been documented within bacterial communities associated with kelps and other seaweed species from around the world and may be important for host function and wider ecosystem health in general.

Bacterial community structure in the rumen and hindgut is associated with nitrogen efficiency in Holstein cows

Nitrogen efficiency (Neff; milk N/N intake) in dairy cows is limited and most of the consumed N is excreted in manure. Despite the crucial role of the gastrointestinal microbiome on N metabolism, associations between bacterial communities at different sections and Neff are not fully elucidated. Enhanced understanding of host-microbiome interactions can provide insights to improve Neff in dairy cows. Twenty-three Holstein cows were selected, and their Neff were determined using a N balance approach. From the cohort of cows, six cows were classified as low Neff and five cows as high Neff and their rumen and fecal bacterial communities were profiled using amplicon sequence variants (ASV) based on 16S rRNA gene sequencing. Then, relationships between differentially abundant bacterial features and Neff were evaluated. Neff in low and high cows averaged 22.8 and 30.3%, respectively. With similar N intake, high Neff cows wasted less N in manure compared to low Neff cows (P < 0.01, 11.0 ± 0.59 vs 14.3 ± 0.54 g of N/kg of milk). Rumen fermentation and plasma profiles were similar between Neff groups, but for plasma Gln which was greater (P = 0.02) in high compared to low Neff cows. In both rumen and feces, the phylogenetic composition of the bacterial communities was similar (P ≥ 0.65) between Neff groups, but differences were observed at the species -level (amplicon sequence variants). In the rumen, differentially abundant species from the genus Prevotella showed strong positive correlations with Neff, whereas in feces, differentially abundant species from the class Clostridia showed strong negative correlations with Neff. Our results revealed that Holstein cows with divergent Neff display distinctive bacterial community structure at the species-level in both the rumen and feces. Strong correlations between differentially abundant species and Neff in both sample sites, support the importance of the rumen bacterial composition on productive responses and suggest a more relevant role of the hindgut microbiome. Targeting both pre- and post-gastric bacterial communities may provide novel opportunities to enhance Neff in dairy cows.

Gut microbiomes of captive primates show phylosymbiosis, respond to dietary sugar reduction, and select for host-specific dietary microbes.

Host-associated microbiomes are influenced by evolutionary history and proximate factors such as diet and environment. Zoos house animals in relatively standardized and manipulatable environments, making zoo populations valuable for studying microbiomes. Using a small population of five, closely related primate species housed under nearly identical environments, we investigated gut microbiome variation regarding (a) congruence between host evolutionary history and gut bacterial composition (i.e. phylosymbiosis), (b) a longitudinal reduction in dietary sugar intake, and (c) ingestion of bacteria from dietary sources. We found that the primate gut microbiomes varied across individuals and showed phylosymbiosis. When animals were fed diets with reduced sugar and increased fibre, we found host-specific changes in taxonomically distinct microbes (Phascolarctobacterium, Megasphaera, and Sharpea). Yet, these bacterial genera share similar functional potential (fibre degradation), indicating that the distinct bacterial communities may fulfill similar functions. Although all individuals received the same diet, the diet-associated bacteria in primate gut microbiomes were distinct across individuals of different species, suggesting a mechanism that selects for unique dietary microbes to persist in animal guts. Our findings show that the microbiomes of a small, captive primate population housed under uniform environmental conditions still show patterns congruent with combined influences of evolutionary history and diet.

Changes in Bacterial Communities and Functions Associated with Litter Degradation During Forest Succession Caused by Forest Disease

Forest succession affects aboveground vegetation and belowground microbial community composition, in which litter degradation plays an important role in nutrient cycling. However, limited information is available on how microbial communities change during litter degradation in forests undergoing succession due to disease. In this study, the bacterial communities and functions in litter degradation during the forest succession from pure Pinus forest (PPF), mixed Pinus and Liquidambar forest (MPF and MLF), and pure Liquidambar forest (PLF) were investigated. The results showed that the bacterial community richness and diversity in both needles or leaves and branch litters increased progressively with forest succession. Proteobacteria, Actinobacteria, Bacteroidetes, and Acidobacteria were the most abundant bacterial phyla in the litter degradation during forest succession. The abundance of Bacteroidetes in branches increased significantly, while the abundance of genus Paraburkholderia decreased during forest succession. The different forests formed distinct bacterial community structures during litter decomposition. Functionally, chemoheterotrophy was the most abundant functional guild, followed by nitrogen fixation, intracellular parasitism, and urealysis. The abundance of nitrogen fixation decreased significantly during forest succession. Similarly, the different forests formed distinct bacterial functional structures in the needle or leaf during the succession. However, only two functional structures were formed in the branch. These results suggest that the bacterial community and its functions undergo significant changes during forest succession, particularly from the pure-pine to mixed-pine forest. These results provide a clear understanding of the changes in bacterial communities and functions during litter degradation in forests undergoing disease-induced succession.

Magnetic-activated cell sorting identifies a unique lung microbiome community

BackgroundThe advent of culture-independent, next-generation DNA sequencing has led to the discovery of distinct lung bacterial communities. Studies of lung microbiome taxonomy often reveal only subtle differences between health and disease, but host recognition and response may distinguish the members of similar bacterial communities in different populations. Magnetic-activated cell sorting has been applied to the gut microbiome to identify the numbers and types of bacteria eliciting a humoral response. We adapted this technique to examine the populations of immunoglobulin-bound bacteria in the lung.MethodsSixty-four individuals underwent bronchoalveolar lavage (BAL). We separated immunoglobulin G-bound bacteria using magnetic-activated cell sorting and sequenced the 16S rRNA gene on the Illumina MiSeq platform. We compared microbial sequencing data in IgG-bound bacterial communities compared to raw BAL then examined the differences in individuals with and without HIV as a representative disease state.ResultsImmunoglobulin G-bound bacteria were identified in all individuals. The community structure differed when compared to raw BAL, and there was a greater abundance of Pseudomonas and fewer oral bacteria in IgG-bound BAL. Examination of IgG-bound communities in individuals with HIV demonstrated the differences in Ig-bound bacteria by HIV status that were not seen in a comparison of raw BAL, and greater numbers of immunoglobulin-bound bacteria were associated with higher pulmonary cytokine levels.ConclusionsWe report a novel application of magnetic-activated cell sorting to identify immunoglobulin G-bound bacteria in the lung. This technique identified distinct bacterial communities which differed in composition from raw bronchoalveolar lavage, revealing the differences not detected by traditional analyses. Cytokine response was also associated with differential immunoglobulin binding of lung bacteria, suggesting the functional importance of these communities.6btME6LTfMPeXYkHvqtMADVideo

Involvement of the 4-coumarate:coenzyme A ligase 4CL4 in rice phosphorus acquisition and rhizosphere microbe recruitment via root growth enlargement.

The 4-coumarate:coenzyme A ligase 4CL4 is involved in enhancing rice P acquisition and use in acid soil by enlarging root growth and boosting functional rhizosphere microbe recruitment. Rice (Oryza sativa L.) cannot easily acquire phosphorus (P) from acid soil, where root growth is inhibited and soil P is fixed. The combination of roots and rhizosphere microbiota is critical for plant P acquisition and soil P mobilization, but the associated molecular mechanism in rice is unclear. 4CL4/RAL1 encodes a 4-coumarate:coenzyme A ligase related to lignin biosynthesis in rice, and its dysfunction results in a small rice root system. In this study, soil culture and hydroponic experiments were conducted to examine the role of RAL1 in regulating rice P acquisition, fertilizer P use, and rhizosphere microbes in acid soil. Disruption of RAL1 markedly decreased root growth. Mutant rice plants exhibited decreased shoot growth, shoot P accumulation, and fertilizer P use efficiency when grown in soil-but not under hydroponic conditions, where all P is soluble and available for plants. Mutant ral1 and wild-type rice rhizospheres had distinct bacterial and fungal community structures, and wild-type rice recruited some genotype-specific microbial taxa associated with P solubilization. Our results highlight the function of 4CL4/RAL1 in enhancing rice P acquisition and use in acid soil, namely by enlarging root growth and boosting functional rhizosphere microbe recruitment. These findings can inform breeding strategies to improve P use efficiency through host genetic manipulation of root growth and rhizosphere microbiota.

New insights on municipal solid waste (MSW) landfill plastisphere structure and function

Plastisphere plays crucial role in global carbon and nitrogen cycles and microplastics formation. Global Municipal Solid Waste (MSW) landfills contain 42 % plastic waste, therefore representing one of the most significant plastispheres. MSW landfills are also the third largest anthropogenic methane sources and the important anthropogenic N2O source. Surprisingly, knowledge of microbiota and the associated microbial carbon and nitrogen cycles of landfill plastispheres is very limited. In this study, we characterized and compared the organic chemicals profile, bacterial community structure and metabolic pathway on plastisphere and the surrounding refuse in a large-scale landfill using GC/MS and 16S rRNA genes high-throughput sequencing, respectively. Landfill plastisphere and the surrounding refuse differed in organic chemicals composition. However, abundant phthalate-like chemicals were determined in both environments, implying the plastics additives leaching. Bacterial colonizing on the plastics surface had significantly higher richness than that in the surrounding refuse. Plastic surface and the surrounding refuse had distinct bacterial community composition. Genera of Sporosarcina, Oceanobacillus and Pelagibacterium were detected on the plastic surface with high abundance, while Ignatzschineria, Paenalcaligenes and Oblitimonas were rich in the surrounding refuse. Typical plastics biodegradation genus Bacillus, Pseudomonas and Paenibacillus were detected in both environments. However, Pseudomonas was dominant in plastic surface (up to 88.73 %), whereas Bacillus was rich in the surrounding refuse (up to 45.19 %). For the carbon and nitrogen cycle, plastisphere was predicted to had significant (P < 0.05) higher functional genes involved in carbon metabolism and nitrification, indicating more activated carbon and nitrogen microbial activity on the plastics surface. Additionally, pH was the main driver in shaping the bacterial community composition on plastic surface. These results indicate that landfill plastispheres serve as unique niches for microbial community habitation and function on microbial carbon and nitrogen cycles. These observations invite further study of the landfill plastispheres ecological effect.

Multiomics Reveals Symbionts, Pathogens, and Tissue-Specific Microbiome of Blacklegged Ticks (Ixodes scapularis) from a Lyme Disease Hot Spot in Southeastern Ontario, Canada.

Ticks in the family Ixodidae are important vectors of zoonoses, including Lyme disease (LD), which is caused by spirochete bacteria from the Borreliella (Borrelia) burgdorferi sensu lato complex. The blacklegged tick (Ixodes scapularis) continues to expand across Canada, creating hot spots of elevated LD risk at the leading edge of its expanding range. Current efforts to understand the risk of pathogen transmission associated with I. scapularis in Canada focus primarily on targeted screens, while natural variation in the tick microbiome remains poorly understood. Using multiomics consisting of 16S metabarcoding and ribosome-depleted, whole-shotgun RNA transcriptome sequencing, we examined the microbial communities associated with adult I. scapularis (n = 32), sampled from four tissue types (whole tick, salivary glands, midgut, and viscera) and three geographical locations within a LD hot spot near Kingston, Ontario, Canada. The communities consisted of both endosymbiotic and known or potentially pathogenic microbes, including RNA viruses, bacteria, and a Babesia sp. intracellular parasite. We show that β-diversity is significantly higher between the bacterial communities of individual tick salivary glands and midguts than that of whole ticks. Linear discriminant analysis effect size (LEfSe) determined that the three potentially pathogenic bacteria detected by V4 16S rRNA sequencing also differed among dissected tissues only, including a Borrelia strain from the B. burgdorferi sensu lato complex, Borrelia miyamotoi, and Anaplasma phagocytophilum. Importantly, we find coinfection of I. scapularis by multiple microbes, in contrast to diagnostic protocols for LD, which typically focus on infection from a single pathogen of interest (B. burgdorferi sensu stricto). IMPORTANCE As a vector of human health concern, blacklegged ticks (Ixodes scapularis) transmit pathogens that cause tick-borne diseases (TBDs), including Lyme disease (LD). Several hot spots of elevated LD risk have emerged across Canada as I. scapularis expands its range. Focusing on a hot spot in southeastern Ontario, we used high-throughput sequencing to characterize the microbiome of whole ticks and dissected salivary glands and midguts. Compared with whole ticks, salivary glands and midguts were more diverse and associated with distinct bacterial communities that are less dominated by Rickettsia endosymbiont bacteria and are enriched for pathogenic bacteria, including a B. burgdorferi sensu lato-associated Borrelia sp., Borrelia miyamotoi, and Anaplasma phagocytophilum. We also found evidence of coinfection of I. scapularis by multiple pathogens. Overall, our study highlights the challenges and opportunities associated with the surveillance of the microbiome of I. scapularis for pathogen detection using metabarcoding and metatranscriptome approaches.

Soil aggregates affect the legacy effect of copper pollution on the microbial communities

Soil aggregates provide spatially heterogeneous microhabitats for microorganisms and their activities. In metal contaminated soil, the microbial community is shaped by both metal stress and aggregate sizes. However, it remains unclear whether and how aggregate sizes affect the legacy effect of metal pollution on microbial communities. Here, we investigated the legacy effect of long-term copper (Cu) pollution on the distribution patterns of the bacterial and protistan communities in soil aggregates. Our results showed that soil aggregates of different sizes possessed distinct bacterial and protistan communities under Cu-polluted and unpolluted conditions (aggregate effects), as reflected by distinct α-diversity and community compositions. The bacterial and protistan communities in micro- and macro-aggregates were more responsive to Cu pollution than those in mega-aggregates, primarily because micro- and macro-aggregates contained a greater number of Cu susceptible bacterial and protistan species. Ciliophora and Chlorophyta displayed great sensitivity to Cu, especially in small aggregate-size fractions, and could serve as a bio-indicator of Cu pollution. Furthermore, the magnitude of aggregate effects on microbial communities was weakened in Cu-polluted soils compared to unpolluted soils. With decreasing aggregate sizes, the co-occurrence networks between bacteria and protists became more complex, connected and compact. Robustness analysis showed that phagotrophic protists played essential roles in sustaining the network stability, especially in mega-aggregates. Our findings highlight the asymmetrical changes in microorganisms in aggregates under long-term Cu pollution, providing a novel insight into the legacy effects of metal pollution on soil microbiomes at the micro-level.

Spatial Succession Underlies Microbial Contribution to Food Digestion in the Gut of an Algivorous Sea Urchin.

Dietary influence on the microbiome in algivorous sea urchins such as Tripneustes gratilla elatensis suggests a bacterial contribution to the digestion of fiber-rich seaweed. An ecological insight into the spatial arrangement in the gut bacterial community will improve our knowledge of host-microbe relations concerning the involved taxa, their metabolic repertoire, and the niches of activity. Toward this goal, we investigated the bacterial communities in the esophagus, stomach, and intestine of Ulva-fed sea urchins through 16S rRNA amplicon sequencing, followed by the prediction of their functional genes. We revealed communities with distinct features, especially those in the esophagus and intestine. The esophageal community was less diverse and was poor in food digestive or fermentation genes. In contrast, bacteria that can contribute to the digestion of the dietary Ulva were common in the stomach and intestine and consisted of genes for carbohydrate decomposition, fermentation, synthesis of short-chain fatty acids, and various ways of N and S metabolism. Bacteroidetes and Firmicutes were found as the main phyla in the gut and are presumably also necessary in food digestion. The abundant sulfate-reducing bacteria in the stomach and intestine from the genera Desulfotalea, Desulfitispora, and Defluviitalea may aid in removing the excess sulfate from the decomposition of the algal polysaccharides. Although these sea urchins were fed with Ulva, genes for the degradation of polysaccharides of other algae and plants were present in this sea urchin gut microbiome. We conclude that the succession of microbial communities along the gut obtained supports the hypothesis on bacterial contribution to food digestion. IMPORTANCE Alga grazing by the sea urchin Tripneustes gratilla elatensis is vital for nutrient recycling and constructing new reefs. This research was driven by the need to expand the knowledge of bacteria that may aid this host in alga digestion and their phylogeny, roles, and activity niches. We hypothesized alterations in the bacterial compositional structure along the gut and their association with the potential contribution to food digestion. The current spatial insight into the sea urchin's gut microbiome ecology is novel and reveals how distinct bacterial communities are when distant from each other in this organ. It points to keynote bacteria with genes that may aid the host in the digestion of the complex sulfated polysaccharides in dietary Ulva by removing the released sulfates and fermentation to provide energy. The gut bacteria's genomic arsenal may also help to gain energy from diets of other algae and plants.

A metagenomics approach to characterize the footrot microbiome in Merino sheep

In the Portuguese Alentejo region, Merino sheep breed is the most common breed, reared for the production of meat, dairy, and wool. Footrot is responsible for lameness, decreased animal welfare, and higher production losses, generating a negative economic impact. The disease is caused by Dichelobacter nodosus that interacts with the sheep foot microbiome, to date largely uncharacterized. In fact, Dichelobacter nodosus is not able to induce footrot by itself being required the presence of a second pathogen known as Fusobacterium necrophorum. To understand and characterize the footrot microbiome dynamics of different footrot lesion scores, a whole metagenome sequencing (WMGS) approach was used. Foot tissue samples were collected from 212 animals with different degrees of footrot lesion scores, ranging from 0 to 5. Distinct bacterial communities were associated with feet with different footrot scores identifying a total of 63 phyla and 504 families. As the severity of footrot infection increases the microorganisms’ diversity decreases triggering a shift in the composition of the microbiome from a dominant gram-positive in mild stages to a dominant gram-negative in the severe stages. Several species previously associated with footrot and other polymicrobial diseases affecting the epidermis and provoking inflammatory responses such as Treponema spp., Staphylococcus spp., Streptococcus spp. and Campylobacter spp. were identified proliferating along with the lesions’ severity. Although these bacteria are not able to initiate footrot, several evidences have been described supporting their association with the severity and incidence increase of footrot lesions caused by Dichelobacter nodosus and Fusobacterium necrophorum. Further investigation is required to establish the roles of particular taxa and identify which of them play a role in the disease process and which are opportunistic pathogens.

Bacterial microbiome in tropical lichens and the effect of the isolation method on culturable lichen-derived actinobacteria

Ten samples of tropical lichens collected from Doi Inthanon, Thailand, were explored for the diversity of their bacterial microbiomes through 16S rRNA-based metagenomics analysis. The five predominant lichen-associated bacteria belonged to the phyla Proteobacteria (31.84%), Planctomycetota (17.08%), Actinobacteriota (15.37%), Verrucomicrobiota (12.17%), and Acidobacteriota (7.87%). The diversity analysis metric showed that Heterodermia contained the highest bacterial species richness. Within the lichens, Ramalina conduplicans and Cladonia rappii showed a distinct bacterial community from the other lichen species. The community of lichen-associated actinobacteria was investigated as a potential source of synthesized biologically active compounds. From the total Operational Taxonomic Units (OTUs) found across the ten different lichen samples, 13.21% were identified as actinobacteria, including the rare actinobacterial genera that are not commonly found, such as Pseudonocardia, Kineosporia, Dactylosporangium, Amycolatopsis, Actinoplanes, and Streptosporangium. Evaluation of the pretreatment method (heat, air-drying, phenol, and flooding) and isolation media used for the culture-dependent actinobacterial isolation revealed that the different pretreatments combined with different isolation media were effective in obtaining several species of actinobacteria. However, metagenomics analyses revealed that there were still several strains, including rare actinobacterial species, that were not isolated. This research strongly suggests that lichens appear to be a promising source for obtaining actinobacteria.

Inter- and intraspecific phytochemical variation correlate with epiphytic flower and leaf bacterial communities.

Microbes associated with flowers and leaves affect plant health and fitness and modify the chemical phenotypes of plants with consequences for interactions of plants with their environment. However, the drivers of bacterial communities colonizing above-ground parts of grassland plants in the field remain largely unknown. We therefore examined the relationships between phytochemistry and the epiphytic bacterial community composition of flowers and leaves ofRanunculus acris and Trifolium pratense. On 252 plant individuals, we characterized primary and specialized metabolites, that is, surface sugars, volatile organic compounds (VOCs), and metabolic fingerprints, as well as epiphytic flower and leaf bacterial communities. The genomic potential of bacterial colonizers concerning metabolic capacities was assessed using bacterial reference genomes. Phytochemical composition displayed pronounced variation within and between plant species and organs, which explained part of the variation in bacterial community composition. Correlation network analysis suggests strain-specific correlations with metabolites. Analysis of bacterial reference genomes revealed taxon-specific metabolic capabilities that corresponded with genes involved in glycolysis and adaptation to osmotic stress. Our results show relationships between phytochemistry and the flower and leaf bacterial microbiomes suggesting that plants provide chemical niches for distinct bacterial communities. In turn, bacteria may induce alterations in the plants' chemical phenotype. Thus, our study may stimulate further research on the mechanisms of trait-based community assembly in epiphytic bacteria.

The role of inherited characteristics from parent materials in shaping bacterial communities in agricultural soils

Parent materials are crucial in soil formation and development, but their importance in shaping soil bacterial communities after thousands of years of soil formation remains unknown, especially in agricultural soils. To resolve the influence of underlying features inherited from parent materials on soil microbiome, the microbial community in 197 agricultural soils with long-term crop cultivation history and nonagricultural reference soils from four major types of soils in China, i.e., quaternary red clay soils, tertiary red sandstone soils, alluvial soils and black soils, were analyzed and compared. We found that different types of soils supported distinct bacterial communities. The characteristics inherited from parent materials explained more of the variation (31.47%) in bacterial community structure than the selected variables regulated by soil management (1.63%) and the climate condition (1.10%). Only 9.0% of total bacterial amplicon sequence variants (ASVs) which contributed, on average, 47% of the total bacterial abundances in a given agricultural soil, were shared by all soil types. These abundant common ASVs were closely related to agricultural practices, suggesting a strong enrichment effect of a small number of core taxa by long-term crop cultivation. In contrast, approximately 55.6% of ASVs with low relative abundance were specific to soil type. These specific groups were closely associated with the distinctive features of soil type, implying that they represent unique populations selected by the parent material features during pedogenesis. Collectively, soil type may have a strong selective pressure on the bacterial communities in matured agricultural soils, leading to a large pool of specific taxa with limited environmental occurrence. Whilst a small number of core taxa achieve high abundances by responding to long-term crop cultivation.

Multiple facets of cutting-edge mycorrhizal research: 11th International Conference on Mycorrhiza (ICOM 11), Beijing, China, August 2022: 11th International Conference on Mycorrhiza (ICOM 11), Beijing, China, 1-5 August 2022.

Multiple facets of cutting-edge mycorrhizal research: 11th International Conference on Mycorrhiza (ICOM 11), Beijing, China, August 2022: 11th International Conference on Mycorrhiza (ICOM 11), Beijing, China, 1-5 August 2022.

Soil amendment with insect exuviae causes species-specific changes in the rhizosphere bacterial community of cabbage plants

Insect exuviae are a chitin-rich by-product of insect farming that is considered to have great potential for contributing to sustainable agriculture. When used as soil amendment, insect exuviae have been suggested to promote plant growth and health by stimulating naturally occurring beneficial microbes. In a greenhouse experiment, the exuviae of black soldier fly larvae (Hermetia illucens L.), house crickets (Acheta domesticus L.), and yellow mealworms (Tenebrio molitor L.) were added to soil from an organically managed field. Brussels sprouts, Brassica oleracea L., plants were grown in amended soil to assess effects on plant growth and investigate bacterial abundance, diversity, and community composition in the rhizosphere. All soil amendments increased plant shoot biomass and stimulated bacterial growth. At the same time, bacterial diversity was diminished and the different amendments resulted in distinct bacterial communities. Most notably, soil amendment with house cricket exuviae increased the relative abundances of the genera Lysinibacillus and Paenibacillus, whereas the other amendments did not. The exuviae of black soldier fly larvae, however, stimulated the genus Pseudomonas and different genera belonging to the Burkholderiaceae for a longer period of time than the exuviae of either other insect species. In view of the differential enrichment of potentially plant growth-promoting or plant-protective bacteria, soil amendments with the exuviae of different insect species might have specific uses in agriculture. The present study provides a basis for investigating the combined application of insect exuviae with beneficial bacteria that are commonly used in crop production.

Distinct Bacterial Communities in São Jorge Cheese with Protected Designation of Origin (PDO)

São Jorge cheese is an iconic product of the Azores, produced from raw cow's milk and natural whey starter (NWS). Although it is produced according to Protected Designation of Origin (PDO) specifications, the granting of the PDO label depends crucially on sensory evaluation by trained tasters. The aim of this work was to characterize the bacterial diversity of this cheese using next-generation sequencing (NGS) and to identify the specific microbiota that contributes most to its uniqueness as a PDO by distinguishing the bacterial communities of PDO and non-PDO cheeses. The NWS and curd microbiota was dominated by Streptococcus and Lactococcus, whereas Lactobacillus and Leuconostoc were also present in the core microbiota of the cheese along with these genera. Significant differences (p < 0.05) in bacterial community composition were found between PDO cheese and non-certified cheese; Leuconostoc was found to play the chief role in this regard. Certified cheeses were richer in Leuconostoc, Lactobacillus and Enterococcus, but had fewer Streptococcus (p < 0.05). A negative correlation was found between contaminating bacteria, e.g., Staphylococcus and Acinetobacter, and the development of PDO-associated bacteria such as Leuconostoc, Lactobacillus and Enterococcus. A reduction in contaminating bacteria was found to be crucial for the development of a bacterial community rich in Leuconostoc and Lactobacillus, thus justifying the PDO seal of quality. This study has helped to clearly distinguish between cheeses with and without PDO based on the composition of the bacterial community. The characterization of the NWS and the cheese microbiota can contribute to a better understanding of the microbial dynamics of this traditional PDO cheese and can help producers interested in maintaining the identity and quality of São Jorge PDO cheese.

Estuarine Sediment Microbiomes from a Chronosequence of Restored Urban Salt Marshes.

Salt marshes play an important role in the global nutrient cycle. The sediments in these systems harbor diverse and complex bacterial communities possessing metabolic capacities that provide ecosystem services such as nutrient cycling and removal. On the East Coast of the USA, salt marshes have been experiencing degradation due to anthropogenic stressors. Salt marsh islands within Jamaica Bay, New York City (USA), are surrounded by a large highly urbanized watershed and have declined in area. Restoration efforts have been enacted to reduce further loss, but little is known about how microbial communities develop following restoration activities, or how processes such as nitrogen cycling are impacted. Sediment samples were collected at two sampling depths from five salt marsh islands to characterize the bacterial communities found in marsh sediment including a post-restoration chronosequence of 3-12 years. We used 16s rRNA amplicon sequencing to define alpha and beta diversity, taxonomic composition, and predicted metabolic profile of each sediment sample. We found significant differences in alpha diversity between sampling depths, and significant differences in beta diversity, taxonomic composition, and predicted metabolic capacity among the five sampling locations. The youngest restored site and the degraded natural sampling site exhibited the most distinct communities among the five sites. Our findings suggest that while the salt marsh islands are located in close proximity to each other, they harbor distinct bacterial communities that can be correlated with post-restoration age, marsh health, and other environmental factors such as availability of organic carbon. IMPORTANCE: Salt marshes play a critical role in the global nutrient cycle due to sediment bacteria and their metabolic capacities. Many East Coast salt marshes have experienced significant degradation over recent decades, thought largely to be due to anthropogenic stressors such as nitrogen loading, urban development, and sea-level rise. Salt marsh islands in Jamaica Bay (Queens/Brooklyn NY) are exposed to high water column nitrogen due to wastewater effluent. Several receding marsh islands have been subjected to restoration efforts to mitigate this loss. Little is known about the effect marsh restoration has on bacterial communities, their metabolic capacity, or how they develop post-restoration. Here, we describe the bacterial communities found in marsh islands including a post-restoration chronosequence of 3-12 years and one degraded marsh island that remains unrestored. We found distinct communities at marsh sites, despite their geographic proximity. Differences in diversity and community composition were consistent with changes in organic carbon availability that occur during marsh development, and may result in differences in ecosystem function among sites.

Carrot genotypes differentially alter soil bacterial communities and decomposition of plant residue in soil

PurposeFarmers need alternative approaches to manage nitrogen (N) that meet crop needs while reducing loss to the environment. Identifying crop genotypes that promote decomposition of organic materials and understanding the potential mechanisms responsible could help address this challenge. Consequently, we aimed to 1) determine whether carrot genotypes differ in their potential to facilitate organic matter decomposition in soil, and 2) identify bacterial taxa that are stimulated by carrot roots, and thus could play a role in these processes.MethodsWe grew five genotypes expected to differ in N use efficiency in a nutrient-poor soil amended with 15 N-enriched corn residue, tracked changes in carbon (C) and N pools, quantified microbial activity and bacterial community composition, and predicted the potential expression of microbial genes involved in soil C and N cycles.ResultsExperimental genotype 8503 had the greatest capacity to promote decomposition of corn residues. This genotype had the highest % of N from the corn residue in its taproots and on average, promoted higher b-glucosidase activity in soils. Distinct bacterial communities from the families Micromonosporaceae, Chromatiaceae, and Rhodospirillaceae were also enriched in the soils of genotypes like 8503 that were most effective in obtaining N from the corn residue, and this was correlated with greater potential expression of genes responsible for β-glucosidase and nitrification activity.ConclusionsCarrot genotypes do differ in their potential to alter soil bacterial communities and stimulate microbially-mediated decomposition of organic materials indicating that it may be possible to begin selecting for this important trait.

Nitrifier Assemblages and Dynamics in Secondary Water Supply Systems: Predominance of Comammox Nitrospira in Tank Biofilm and Sediment

Nitrifiers in chloraminated drinking water distribution systems can trigger severe nitrification, resulting in subsequent water quality deteriorations. However, the occurrence and dynamics of nitrifiers in secondary water supply systems (SWSSs), an important water supply component beyond the distribution mains, remain largely unexplored. This study investigated the density, distribution, and diversities of nitrifiers in different microbial habitats (water, biofilm, and sediment) in SWSSs with different characteristics. Quantitative polymerase chain reaction analysis indicated higher gene copy numbers of ammonia-oxidizing archaea, ammonia-oxidizing bacteria, comammox clade A, and strict nitrite-oxidizing bacteria in SWSSs relative to the distribution mains (1.3–2.1 log10GC/mL increase, P < 0.05). Comammox were preferentially enriched in biofilm and sediments of SWSS tanks, highlighting biofilm and sediment as important ecological niches for comammox. Illumina sequencing of 16S rRNA genes revealed the presence of diverse nitrifiers (e.g., Nitrospira, Nitrosomonas, Nitrotoga, and Nitrobacter) in SWSSs, with distinct bacterial nitrifier communities noted in SWSS water compared to the distribution main water (analysis of similarity (ANOSIM), P < 0.05). Different bacterial nitrifier communities were noted between water and sediments in SWSS tanks, indicating niche segregations of nitrifiers (ANOSIM, P < 0.05). The results highlight SWSS as an important reservoir of nitrifiers and provide insights into nitrification monitoring and control strategies in SWSSs.