Members Of Bacterial Community Research Articles

Experimental Study on Ecological and Biogeochemical Role of Calcimycocavites in Understanding Carbon Fluxes in the Age of Global Warming and Climate Change

The present work reports the results of calcimycocavitological studies on the seashells from beaches of north Goa, India yielding distinct microfungal forms known as calcimycocavites which are important in global climate change studies. SEM studies of the calcareous shell fragments revealed the micro tunneling behavior of the fungi. Digital analysis of SEM images using Mountain Premium 7.2 software revealed the fine topography of calcimycocavites hyphae along with unidentified presumptive biomineral encrustations. The biodegradation of mycocavitogenic insoluble Calcium Oxalate by oxalotrophic members of bacterial communities may occur using bacterial Oxalate decarboxylase and formate dehydrogenase finally releasing Carbon Di Oxide and water and Calcium oxide to the local nutrient pool. Calcimycocavites may be thus involved in the biogeochemical cycling of Carbon and Calcium in the Ocean-Beach environment. The ecological, biological, and biogeochemical implications of the findings are presented concerning the possible role of calcimycocavites in Calcium and Carbon cycling by breakdown of the calcareous shells and release of inorganic and organic components in the ecosystem. The role of calcimycocavites is stressed in global climate studies.

Impacts of climate-driven upwelling intensification on the microbiota and health of cultivated scallops

The scallop Argopecten purpuratus plays a pivotal role as an economic resource cultivated in regions where climate change may intensify the coastal upwelling. This process has the potential to impact host-microbiota interactions. Hence, we conducted a field study to investigate the effects of varying upwelling intensities on hemolymph and gill microbiota dynamics (utilizing 16S rRNA gene sequencing), as well as the pathological state of A. purpuratus maintained in culture systems. Helicobactereaceae and Arcobactereaceae emerged as the prevailing families within both the hemolymph and gills. In contrast to the period of weak upwelling, the phase characterized by intensified upwelling revealed notable shifts in the abundance of bacterial community members, thereby leading to implications for the functional potential of the hemolymph microbiota. Notably, environmental factors played a substantial role in shaping the microbial community, accounting for 82–96% of the observed variation. Among these factors, wind, oxygen, and temperature exerted the most influence. During intensified upwelling, the abundance of Arcobactereaceae increased from 27% to 36% within gills and from 43% to 55% within hemolymph. Conversely, Helicobactereaceae decreased, particularly within gills, from 15% to 8% during the same period. Significantly, bacteria with fermentation capabilities, such as Colwellia, along with those involved in sulfur cycle processes, such as Arcobactereaceae, Desulfobulbaceae, and Desulfobacteraceae, exhibited an elevated representation during the period of intensified upwelling. This suggests potential nutritional advantages for A. purpuratus. However, the intense upwelling phase also saw an overrepresentation of potentially pathogenic bacteria for mollusks, including Francisella halioticida, Vibrio, and Photobacterium. Moreover, histopathological examination revealed heightened hemocytic infiltration, the presence of granulomatous “swirl” lesions, and a potential Apicomplexan parasite during this intensified upwelling period. These findings underscore the importance of the adaptability of host-microbiota interactions and the potential risks of pathogenicity for cultivated A. purpuratus within the context of ongoing and future environmental changes. Therefore, continuous monitoring of pathogen emergence and immune status evaluation during intensified upwelling periods are crucial for successful A. purpuratus aquaculture.

Lipopeptides as rhizosphere public goods for microbial cooperation.

Here, we provide new insights into the possible fate of cyclic lipopeptides as prominent specialized metabolites from beneficial bacilli and pseudomonads once released in the soil. Our data illustrate how the B. velezensis lipopeptidome may be enzymatically remodeled by Streptomyces as important members of the soil bacterial community. The enzymatic arsenal of S. venezuelae enables an unsuspected extensive degradation of these compounds, allowing the bacterium to feed on these exogenous products via a mechanism going beyond linearization, which was previously reported as a detoxification strategy. As soils are carbon-rich and nitrogen-poor environments, we propose a new role for cyclic lipopeptides in interspecies interactions, which is to fuel the nitrogen metabolism of a part of the rhizosphere microbial community. Streptomyces and other actinomycetes, producing numerous peptidases and displaying several traits of beneficial bacteria, should be at the front line to directly benefit from these metabolites as "public goods" for microbial cooperation.

A comparison of the infant gut microbiome before versus after the start of the covid-19 pandemic

The COVID-19 pandemic and resulting public health directives led to many changes in families’ social and material environments. Prior research suggests that these changes are likely to impact composition of the gut microbiome, particularly during early childhood when the gut microbiome is developing most rapidly. Importantly, disruption to the gut microbiome during this sensitive period can have potentially long-lasting impacts on health and development. In the current study, we compare gut microbiome composition among a socioeconomically and racially diverse group of 12-month old infants living in New York City who provided stool samples before the pandemic (N = 34) to a group who provided samples during the first 9-months of the pandemic (March–December 2020; N = 20). We found that infants sampled during the pandemic had lower alpha diversity of the microbiome, lower abundance of Pasteurellaceae and Haemophilus, and significantly different beta diversity based on unweighted Unifrac distance than infants sampled before the pandemic. Exploratory analyses suggest that gut microbiome changes due to the pandemic occurred relatively quickly after the start of the pandemic and were sustained. Our results provide evidence that pandemic-related environmental disruptions had an impact on community-level taxonomic diversity of the developing gut microbiome, as well as abundance of specific members of the gut bacterial community.

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

Soil respiration in response to biotic and abiotic factors under different mulching measures on rain-fed farmland

Mulching measures strongly affect the soil physicochemical properties and crop growth. However, the effects of crop growth and the soil environment under mulching on soil respiration (Rs) and its components (Rh: heterotrophic respiration; Ra: autotrophic respiration) are still unclear. Therefore, in this study, we conducted an experiment in a maize field for five consecutive years with different mulching measures in a rain-fed area of China (P: flat planting with full plastic film mulching; R: ridge–furrow with half plastic film mulching; S: flat planting with full straw mulching; and CK: conventional tillage without mulching). The changes in the Rs, Rh, Ra, soil physicochemical properties, and microbial communities were monitored. The results showed that compared with CK, Rs increased by 37.4% under P, 20.3% under R, and 24.6% under S, and Rh and Ra increased by 768–1257 kg C ha–1 year–1 and 278–678 kg C ha–1 year–1, respectively. Among all of the treatments, the largest increases in the soil respiration emission fluxes and their components occurred under P. Plastic film mulching (P and R) significantly increased the aboveground biomass, leaf area index (LAI), root biomass, and grain yield in maize, whereas S had different effects on maize growth in different years. In addition, mulching significantly changed the soil physicochemical properties comprising the soil temperature, soil water content, NO3–, dissolved organic carbon, and microbial biomass carbon. Structural equation modeling showed that these physicochemical properties explained 89% of the variability in Ra and 71% of the variability in Rh. In addition, the changes in the Rs, Rh, and Ra rates were influenced by the soil bacterial diversity (Shannon diversity) and relative abundances of certain bacterial community members (Proteobacteria, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Firmicutes). In summary, our results demonstrate that the Rs components were strongly influenced by SWC, ST, NO3–, and the soil microbial community. In particular, the increased soil carbon emissions under mulching were mainly due to Rh, and Rh was highly sensitive to the changes in precipitation. P obtained the highest soil carbon emissions and maize yield among all treatments, whereas S had a poor effect on increasing the yield. Considering climate warming and food security issues, R performed best.

LaeA-Regulated Fungal Traits Mediate Bacterial Community Assembly.

Potent antimicrobial metabolites are produced by filamentous fungi in pure culture, but their ecological functions in nature are often unknown. Using an antibacterial Penicillium isolate and a cheese rind microbial community, we demonstrate that a fungal specialized metabolite can regulate the diversity of bacterial communities. Inactivation of the global regulator, LaeA, resulted in the loss of antibacterial activity in the Penicillium isolate. Cheese rind bacterial communities assembled with the laeA deletion strain had significantly higher bacterial abundances than the wild-type strain. RNA-sequencing and metabolite profiling demonstrated a striking reduction in the expression and production of the natural product pseurotin in the laeA deletion strain. Inactivation of a core gene in the pseurotin biosynthetic cluster restored bacterial community composition, confirming the role of pseurotins in mediating bacterial community assembly. Our discovery demonstrates how global regulators of fungal transcription can control the assembly of bacterial communities and highlights an ecological role for a widespread class of fungal specialized metabolites. IMPORTANCE Cheese rinds are economically important microbial communities where fungi can impact food quality and aesthetics. The specific mechanisms by which fungi can regulate bacterial community assembly in cheeses, other fermented foods, and microbiomes in general are largely unknown. Our study highlights how specialized metabolites secreted by a Penicillium species can mediate cheese rind development via differential inhibition of bacterial community members. Because LaeA regulates specialized metabolites and other ecologically relevant traits in a wide range of filamentous fungi, this global regulator may have similar impacts in other fungus-dominated microbiomes.

Bacterial Communities Are Less Diverse in a Strepsipteran Endoparasitoid than in Its Fruit Fly Hosts and Dominated by Wolbachia

Microbiomes play vital roles in insect fitness and health and can be influenced by interactions between insects and their parasites. Many studies investigate the microbiome of free-living insects, whereas microbiomes of endoparasitoids and their interactions with parasitised insects are less explored. Due to their development in the constrained environment within a host, endoparasitoids are expected to have less diverse yet distinct microbiomes. We used high-throughput 16S rRNA gene amplicon sequencing to characterise the bacterial communities of Dipterophagus daci (Strepsiptera) and seven of its tephritid fruit fly host species. Bacterial communities of D. daci were less diverse and contained fewer taxa relative to the bacterial communities of the tephritid hosts. The strepsipteran’s microbiome was dominated by Pseudomonadota (formerly Proteobacteria) (> 96%), mainly attributed to the presence of Wolbachia, with few other bacterial community members, indicative of an overall less diverse microbiome in D. daci. In contrast, a dominance of Wolbachia was not found in flies parasitised by early stages of D. daci nor unparasitised flies. Yet, early stages of D. daci parasitisation resulted in structural changes in the bacterial communities of parasitised flies. Furthermore, parasitisation with early stages of D. daci with Wolbachia was associated with a change in the relative abundance of some bacterial taxa relative to parasitisation with early stages of D. daci lacking Wolbachia. Our study is a first comprehensive characterisation of bacterial communities in a Strepsiptera species together with the more diverse bacterial communities of its hosts and reveals effects of concealed stages of parasitisation on host bacterial communities.

Storage and Algal Association of Bacteria That Protect Microchloropsis salina from Grazing by Brachionus plicatilis.

Loss of algal production from the crashes of algal mass cultivation systems represents a significant barrier to the economic production of microalgal-based biofuels. Current strategies for crash prevention can be too costly to apply broadly as prophylaxis. Bacteria are ubiquitous in microalgal mass production cultures, however few studies investigate their role and possible significance in this particular environment. Previously, we demonstrated the success of selected protective bacterial communities to save Microchloropsis salina cultures from grazing by the rotifer Brachionus plicatilis. In the current study, these protective bacterial communities were further characterized by fractionation into rotifer-associated, algal-associated, and free-floating bacterial fractions. Small subunit ribosomal RNA amplicon sequencing was used to identify the bacterial genera present in each of the fractions. Here, we show that Marinobacter, Ruegeria, and Boseongicola in algae and rotifer fractions from rotifer-infected cultures likely play key roles in protecting algae from rotifers. Several other identified taxa likely play lesser roles in protective capability. The identification of bacterial community members demonstrating protective qualities will allow for the rational design of microbial communities grown in stable co-cultures with algal production strains in mass cultivation systems. Such a system would reduce the frequency of culture crashes and represent an essentially zero-cost form of algal crop protection.

Dysbiosis of the larval gut microbiota of Spodoptera frugiperda strains feeding on different host plants

The gut microbiota plays important roles in the bioecology of insects, including host plant adaptation and speciation. Spodoptera frugiperda has two well-established host-adapted strains with marked differences at the genetic and host plant utilization levels. We investigated whether differences in the gut microbiota would occur between the “corn” (CS) and “rice” (RS) strains of S. frugiperda when feeding on different crops. The gut microbiota of larvae fed on corn and millet was predominantly represented by Firmicutes followed by Proteobacteria, with an opposite pattern in larvae fed on cotton. No differences were observed in the diversity of the gut microbiota community between RS and CS using PERMANOVA. PCoA analyses resulted in distinct bacterial clusters based on the host plant. Comparisons of the gut microbiota between CS and RS at the phylum level resulted in differences only for larvae fed on cotton plants. However, differences in relative abundance of bacteria at the genus level in the microbiota of CS and RS were observed regardless of the food source used. We also found differences in the potential functional contribution of bacteria between the strains. In conclusion the gut microbiota of S. frugiperda is strongly modulated by the host plant while strains seemed to play a minor role in changing the abundance of members of the gut bacterial community.

Crop rotation-driven change in physicochemical properties regulates microbial diversity, dominant components, and community complexity in paddy soils

Crop rotation is a production practice to promote a more diversified plant community in rice field, thereby enhancing agroecosystem sustainability and production efficiency under an increasing demand for food and energy. The regulation of rotations of rice with different crop on soil microbiomes and their relationships with key soil physicochemical drivers has not been understood enough. To address this, soils of 0–20 cm and 20–40 cm layers subjected to four rotation regimes (rice-rice, tobacco-rice, rice-oilseed rape, and rice-rice-oilseed rape) were collected from a long-term (>20 year) field experiment. Compared with the rice-rice, the other three rotations significantly increased surface soil porosity and the content of soil total nitrogen (N), available phosphorus (P), total potassium, and organic matter, as well as improved soil aggregate composition but decreased soil bulk density (P < 0.05). Rotation patterns and soil layers independently or interactively explained the variation in microbial diversity and community composition in soil, with a greater impact of the rotation regimes (9.3–49.7%; P < 0.05). The rotation systems of rice-oilseed rape and rice-rice-oilseed rape showed a higher soil microbial diversity and co-occurrence of the community species compared with other two systems. The components of the genus Clostridium, Pedobacter, and Gp1 were the dominant hubs (with a larger number of edges) in bacterial communities, and the members of the Mortierella, Ascomycota, and Agaricales were the hubs in fungal communities. The co-occurring networks between the members of bacterial and fungal communities in the four systems showed same keystone taxa that mainly belong to fungal genus Mortierella, Fusicolla, Paranamyces, and Pseudeurotium. The microbial diversity and community composition were positively correlated with soil NH4+-N-to-NO3--N ratio, available P content, total N content, and soil aggregates, and meanwhile, those variables were the creadible predictors of the community changes. These findings highlighted the advantage of rice rotations with oilseed rape in improvement of soil fertility and production by mediating soil microbiome and physicochemical property relationships.

Effects of Fluticasone Propionate on Klebsiella pneumoniae and Gram-Negative Bacteria Associated with Chronic Airway Disease.

Inhaled corticosteroids (ICS) are commonly prescribed first-line treatments for asthma and chronic obstructive pulmonary disease (COPD). Recent evidence has shown that ICS use is associated with changes in the airway microbiome, which may impact clinical outcomes such as potential increased risk for pneumonia in COPD. Although the immunomodulatory effects of corticosteroids are well appreciated, whether ICS could directly influence the behavior of respiratory tract bacteria has been unknown. In this pilot study we explored the effects of fluticasone proprionate, a commonly prescribed inhaled corticosteroid, on respiratory bacteria with an expanded focus on Klebsiella pneumoniae, a species previously implicated in fluticasone-associated pneumonia in COPD. We observed significant effects of fluticasone proprionate on growth responses of K. pneumoniae, as well as other bacterial species isolated from asthmatic patients. Fluticasone-exposed K. pneumoniae displayed altered expression of several bacterial genes and reduced the metabolic activity of bronchial epithelial cells and their expression of human β-defensin 2. Targeted assays identified a fluticasone metabolite from fluticasone-exposed K. pneumoniae cells, suggesting this species may be capable of metabolizing fluticasone proprionate. Collectively, these observations support the hypothesis that specific members of the airway microbiota possess the functional repertoire to respond to or potentially utilize corticosteroids in their microenvironment. These findings lay a foundation for novel research directions into the potential direct effects of ICS, often prescribed long term to patients, on the broader airway microbial community and on the behavior of specific microbial species implicated in asthma and COPD outcomes. IMPORTANCE Inhaled corticosteroids are widely prescribed for many respiratory diseases, including asthma and COPD. While they benefit many patients, corticosteroids can also have negative effects. Some patients do not improve with treatment and even experience adverse side effects. Recent studies have shown that inhaled corticosteroids can change the make-up of bacteria in the human respiratory tract. However, whether these medications can directly impact the behavior of such bacteria has been unknown. Here, we explored the effects of fluticasone propionate, a commonly prescribed inhaled corticosteroid, on Klebsiella pneumoniae and other airway bacteria of interest, including primary species isolated from adult asthma patients. We provide evidence of growth responses to direct fluticasone exposure in culture and further examined fluticasone's effects on K. pneumoniae, including gene expression changes and effects of fluticasone-exposed bacteria on airway cells. These findings indicate that members of the human airway bacterial community possess the functional ability to respond to corticosteroids, which may have implications for the heterogeneity of treatment response observed clinically.

Dynamic utilization of low-molecular-weight organic substrates across a microbial growth rate gradient.

Low-molecular-weight organic substances (LMWOSs) are at the nexus between micro-organisms, plant roots, detritus, and the soil mineral matrix. The nominal oxidation state of carbon (NOSC) has been suggested as a potential parameter for modelling microbial uptake rates of LMWOSs and the efficiency of carbon incorporation into new biomass. In this study, we assessed the role of compound class and oxidation state on uptake kinetics and substrate-specific carbon use efficiency (SUE) during the growth of three model soil micro-organisms, a fungal isolate (Penicillium spinulosum) and two bacterial isolates (Paraburkholderia solitsugae, and Ralstonia pickettii). Isolates were chosen that spanned a growth rate gradient (0.046-0.316 h-1 ) in media containing 34 common LMWOSs at realistically low initial concentrations (25 μM each). Clustered, co-utilization of LMWOSs occurred for all three organisms. Potential trends (p < 0.05) for early utilization of more oxidized substrates were present for the two bacterial isolates (P. solitsugae and R. pickettii), but high variability (R2 < 0.15) and a small effect of NOSC indicate these relationships are not useful for prediction. The SUEs of selected substrates ranged from 0.16 to 0.99 and there was no observed relationship between NOSC and SUE. Our results do not provide compelling population-level support for NOSC as a predictive tool for either uptake kinetics or the efficiency of use of LMWOS in soil solution. Metabolic strategies of organisms are likely more important than chemical identity in determining LMWOS cycling in soils. Previous community-level observations may be biased towards fast-responding bacterial community members.

Genome-Resolved Metagenomics Informs the Functional Ecology of Uncultured Acidobacteria in Redox Oscillated Sphagnum Peat.

ABSTRACTUnderstanding microbial niche differentiation along ecological and geochemical gradients is critical for assessing the mechanisms of ecosystem response to hydrologic variation and other aspects of global change. The lineage-specific biogeochemical roles of the widespread phylum Acidobacteria in hydrologically sensitive ecosystems, such as peatlands, are poorly understood. Here, we demonstrate that Acidobacteria sublineages in Sphagnum peat respond differentially to redox fluctuations due to variable oxygen (O2) availability, a typical feature of hydrologic variation. Our genome-centric approach disentangles the mechanisms of niche differentiation between the Acidobacteria genera Holophaga and Terracidiphilus in response to the transient O2 exposure of peat in laboratory incubations. Interlineage functional diversification explains the enrichment of the otherwise rare Holophaga in anoxic peat after transient O2 exposure in comparison to Terracidiphilus dominance in continuously anoxic peat. The observed niche differentiation of the two lineages is linked to differences in their carbon degradation potential. Holophaga appear to be primarily reliant on carbohydrate oligomers and amino acids, produced during the prior period of O2 exposure via the O2-stimulated breakdown of peat carbon, rich in complex aromatics and carbohydrate polymers. In contrast, Terracidiphilus genomes are enriched in diverse respiratory hydrogenases and carbohydrate active enzymes, enabling the degradation of complex plant polysaccharides into monomers and oligomers for fermentation. We also present the first evidence for the potential contribution of Acidobacteria in peat nitrogen fixation. In addition to canonical molybdenum-based diazotrophy, the Acidobacteria genomes harbor vanadium and iron-only alternative nitrogenases. Together, the results better inform the different functional roles of Acidobacteria in peat biogeochemistry under global change.IMPORTANCE Acidobacteria are among the most widespread and abundant members of the soil bacterial community, yet their ecophysiology remains largely underexplored. In acidic peat systems, Acidobacteria are thought to perform key biogeochemical functions, yet the mechanistic links between the phylogenetic and metabolic diversity within this phylum and peat carbon transformations remain unclear. Here, we employ genomic comparisons of Acidobacteria subgroups enriched in laboratory incubations of peat under variable O2 availability to disentangle the lineage-specific functional roles of these microorganisms in peat carbon transformations. Our genome-centric approach reveals that the diversification of Acidobacteria subpopulations across transient O2 exposure is linked to differences in their carbon substrate preferences. We also identify a previously unknown functional potential for biological nitrogen fixation in these organisms. This has important implications for carbon, nitrogen, and trace metal cycling in peat systems.

Microbial Community Compositional Stability in Agricultural Soils During Freeze-Thaw and Fertilizer Stress

Microbial activity persists in cold region agricultural soils during the fall, winter, and spring (i.e., non-growing season) and frozen condition, with peak activity during thaw events. Climate change is expected to change the frequency of freeze-thaw cycles (FTC) and extreme temperature events (i.e, altered timing, extreme heat/cold events) in temperate cold regions, which may hasten microbial consumption of fall-amended fertilizers, decreasing potency come the growing season. We conducted a high-resolution temporal examination of the impacts of freeze-thaw and nutrient stress on microbial communities in agricultural soils across both soil depth and time. Four soil columns were incubated under a climate model of a non-growing season including precipitation, temperature, and thermal gradient with depth over 60 days. Two columns were amended with fertilizer, and two incubated as unamended soil. The impacts of repeated FTC and nutrient stress on bacterial, archaeal, and fungal soil community members were determined, providing a deeply sampled longitudinal view of soil microbial response to non-growing season conditions. Geochemical changes from flow-through leachate and amplicon sequencing of 16S and ITS rRNA genes were used to assess community response. Despite nitrification observed in fertilized columns, there were no significant microbial diversity, core community, or nitrogen cycling population trends in response to nutrient stress. FTC impacts were observable as an increase in alpha diversity during FTC. Community compositions shifted across a longer time frame than individual FTC, with bulk changes to the community in each phase of the experiment. Our results demonstrate microbial community composition remains relatively stable for archaea, bacteria, and fungi through a non-growing season, independent of nutrient availability. This observation contrasts canonical thinking that FTC have significant and prolonged effects on microbial communities. In contrast to permafrost and other soils experiencing rare FTC, in temperate agricultural soils regularly experiencing such perturbations, the response to freeze-thaw and fertilizer stress may be muted by a more resilient community or be controlled at the level of gene expression rather than population turn-over. These results clarify the impacts of winter FTC on fertilizer consumption, with implications for agricultural best practices and modeling of biogeochemical cycling in agroecosystems.

Ecotoxicological effects of a synthetic and a natural insecticide on earthworms and soil bacterial community

• Chlorpyrifos affects the reproduction output and the weight trend of E. foetida . • The earthworms activity favours spinosad degradation in soil. • Comet assay detect early DNA damage by pesticides on earthworms coelomocytes cells. • Pesticide degraders are enriched after application of both insecticides. Earthworms and microbial communities are essential non-target soil organisms that are useful to assess the collateral impact of pesticides. The present paper reports three laboratory experiments performed to investigate the effects of sub-lethal doses of two insecticides, a biologically-derived (spinosad) and a synthetic organophosphate (chlorpyrifos), on earthworm Eisenia foetida and microorganisms in organic soil. The effects were studied in terms of behaviour, reproduction, survival, and DNA damage (comet assay) in earthworms, and Next Generation Sequencing-Illumina was employed to detect the changes in the microbial community. In addition, the influence of earthworms on the degradation kinetics of insecticides and on microbial diversity was evaluated. The weights, reproductive activity and behaviour of earthworms were particularly compromised and followed a dose-dependent trend in chlorpyrifos trials, where the insecticide's degradation wasn't affected by the presence of Eisenia foetida . However, earthworms contributed to spinosad's metabolisation without significantly impacting their health. Early DNA damage was estimated in earthworms exposed to chlorpyrifos, while the impact of spinosad was significant only at the end of the toxicity test. The analysis on the microbial community indicated the buffering effect earthworms had on the bacterial communities starting from earliest sampling until the end of the trial, as well as bacterial community members' degradation response to pesticides over time.

Cross-kingdom interactions and functional patterns of active microbiota matter in governing deadwood decay.

Microbial community members are the primary microbial colonizers and active decomposers of deadwood. This study placed sterilized standardized beech and spruce sapwood specimens on the forest ground of 8 beech- and 8 spruce-dominated forest sites. After 370 days, specimens were assessed for mass loss, nitrogen (N) content and 15N isotopic signature, hydrolytic and lignin-modifying enzyme activities. Each specimen was incubated with bromodeoxyuridine (BrdU) to label metabolically active fungal and bacterial community members, which were assessed using amplicon sequencing. Fungal saprotrophs colonized the deadwood accompanied by a distinct bacterial community that was capable of cellulose degradation, aromatic depolymerization, and N2 fixation. The latter were governed by the genus Sphingomonas, which was co-present with the majority of saprotrophic fungi regardless of whether beech or spruce specimens were decayed. Moreover, the richness of the diazotrophic Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium group was significantly correlated with mass loss, N content and 15N isotopic signature. By contrast, presence of obligate predator Bdellovibrio spp. shifted bacterial community composition and were linked to decreased beech deadwood decay rates. Our study provides the first account of the composition and function of metabolically active wood-colonizing bacterial and fungal communities, highlighting cross-kingdom interactions during the early and intermediate stages of wood decay.

Do amino and fatty acid profiles of pollen provisions correlate with bacterial microbiomes in the mason bee Osmia bicornis?

Bee performance and well-being strongly depend on access to sufficient and appropriate resources, in particular pollen and nectar of flowers, which constitute the major basis of bee nutrition. Pollen-derived microbes appear to play an important but still little explored role in the plant pollen-bee interaction dynamics, e.g. through affecting quantities and ratios of important nutrients. To better understand how microbes in pollen collected by bees may affect larval health through nutrition, we investigated correlations between the floral, bacterial and nutritional composition of larval provisions and the gut bacterial communities of the solitary megachilid bee Osmia bicornis. Our study reveals correlations between the nutritional quality of pollen provisions and the complete bacterial community as well as individual members of both pollen provisions and bee guts. In particular pollen fatty acid profiles appear to interact with specific members of the pollen bacterial community, indicating that pollen-derived bacteria may play an important role in fatty acid provisioning. As increasing evidence suggests a strong effect of dietary fatty acids on bee performance, future work should address how the observed interactions between specific fatty acids and the bacterial community in larval provisions relate to health in O. bicornis. This article is part of the theme issue 'Natural processes influencing pollinator health: from chemistry to landscapes'.

Associations between bacterial communities and microplastics from surface seawater of the Northern Patagonian area of Chile

The presence of microplastics in oceans and coastlines has increased during recent years due anthropogenic activities and represents a serious environmental problem. The establishment and assembly of microbial communities in these microplastics, specifically located near aquaculture activities, is not well understood. In this study, we analyzed unique and core members of bacterial communities attached to microplastics collected from three coastal environments of the South Pacific, which represent low, medium and high anthropogenic activity derived from the aquaculture industry. Microplastics were analyzed with Fourier-transform infrared spectroscopy, scanning electron microscopy, and next-generation sequencing to assess the prevailing microplastics types, and to characterize microbial communities attached to them. We identified four main types of microplastics (polypropylene, polyethylene, nylon and polystyrene) and 3102 Operational Taxonomic Units (OTUs) at the sampled sites, which were dominated by the phylum Cyanobacteria, Bacteroidetes and Proteobacteria (mainly Alpha and Gammaproteobacteria). Similarity index analysis showed that bacterial communities in microplastics differed from those found in the surrounding seawaters, and also that they varied among locations, suggesting a role of the environment and level of anthropogenic activities on the plastisphere taxa. Despite this difference, 222 bacterial OTUs were shared among the three sites representing between 34 and 51% of OTUs of each sampled site, and thus constituted a core microbiome of microplastics. Comparison of the core microbiome with bacterial communities of the surrounding seawater suggested that the plastisphere constituted a selective habitat for diverse microbial communities. Computational predictions also provided evidence of significantly enriched functions in the core microbiome. Co-occurrence networks revealed that putative ecological interactions among microplastics OTUs was dominated by positive correlations. To the best of our knowledge, this is the first study that evaluated the composition of microbial communities found in microplastics from the Patagonia region of the Southern Pacific Ocean.

Airway Microbiota in Patients With Synchronous Multiple Primary Lung Cancer: The Bacterial Topography of the Respiratory Tract.

Microbes and microbiota dysbiosis are correlated with the development of lung cancer; however, the airway taxa characteristics and bacterial topography in synchronous multiple primary lung cancer (sMPLC) are not fully understood. The present study aimed to investigate the microbiota taxa distribution and characteristics in the airways of patients with sMPLC and clarify specimen acquisition modalities in these patients. Using the precise positioning of electromagnetic navigation bronchoscopy (ENB), we analyzed the characteristics of the respiratory microbiome, which were collected from different sites and using different sampling methods. Microbiome predictor variables were bacterial DNA burden and bacterial community composition based on 16sRNA. Eight non-smoking patients with sMPLC in the same pulmonary lobe were included in this study. Compared with other sampling methods, bacterial burden and diversity were higher in surface areas sampled by bronchoalveolar lavage (BAL). Bacterial topography data revealed that the segment with sMPLC lesions provided evidence of specific colonizing bacteria in segments with lesions. After taxonomic annotation, we identified 4863 phylotypes belonging to 185 genera and 10 different phyla. The four most abundant specific bacterial community members detected in the airway containing sMPLC lesions were Clostridium, Actinobacteria, Fusobacterium, and Rothia, which all peaked at the segments with sMPLC lesions. This study begins to define the bacterial topography of the respiratory tract in patients with sMPLC and provides an approach to specimen acquisition for sMPLC, namely BAL fluid obtained from segments where lesions are located.