Development Of Microbial Communities Research Articles

Construction of a beneficial microbes-enriched rhizosphere system assists plants in phytophagous insect defense: current status, challenges and opportunities.

The construction of a plant rhizosphere system enriched with beneficial microbes (BMs) can efficiently help plants defend against phytophagous insects. However, our comprehensive understanding of this approach is still incomplete. In this review, we methodically analyzed the progress made over the last decade, identifying both challenges and opportunities. The main methods for developing a BMs-enriched rhizosphere system include inoculating exogenous BMs into plants, amending the existing soil microbiomes with amendments, and utilizing plants to shape the soil microbiomes. BMs can assist plants in suppressing phytophagous insects across many orders, including 13 Lepidoptera, seven Homoptera, five Hemiptera, five Coleoptera, four Diptera, and one Thysanoptera species by inducing plant systemic resistance, enhancing plant tolerance, augmenting plant secondary metabolite production, and directly suppressing herbivores. Context-dependent factors such as abiotic and biotic conditions, as well as the response of insect herbivores, can affect the outcomes of BM-assisted plant defense. Several challenges and opportunities have emerged, including the development of synthetic microbial communities for herbivore control, the integration of biosensors for effectiveness assessment, the confirmation of BM targets for phytophagous insect defense, and the regulation of outcomes via smart farming with artificial intelligence. This study offers valuable insights for developing a BM-enriched rhizosphere system within an integrated pest management approach. © 2024 Society of Chemical Industry.

Construction of a beneficial microbes-enriched rhizosphere system assists plants in phytophagous insect defense: current status, challenges and opportunities.

The construction of a plant rhizosphere system enriched with beneficial microbes (BMs) can efficiently help plants defend against phytophagous insects. However, our comprehensive understanding of this approach is still incomplete. In this review, we methodically analyzed the progress made over the last decade, identifying both challenges and opportunities. The main methods for developing a BMs-enriched rhizosphere system include inoculating exogenous BMs into plants, amending the existing soil microbiomes with amendments, and utilizing plants to shape the soil microbiomes. BMs can assist plants in suppressing phytophagous insects across many orders, including 13 Lepidoptera, seven Homoptera, five Hemiptera, five Coleoptera, four Diptera, and one Thysanoptera species by inducing plant systemic resistance, enhancing plant tolerance, augmenting plant secondary metabolite production, and directly suppressing herbivores. Context-dependent factors such as abiotic and biotic conditions, as well as the response of insect herbivores, can affect the outcomes of BM-assisted plant defense. Several challenges and opportunities have emerged, including the development of synthetic microbial communities for herbivore control, the integration of biosensors for effectiveness assessment, the confirmation of BM targets for phytophagous insect defense, and the regulation of outcomes via smart farming with artificial intelligence. This study offers valuable insights for developing a BM-enriched rhizosphere system within an integrated pest management approach. © 2024 Society of Chemical Industry.

Strain‐dependent and host genotype–dependent priority effects in gut microbiome assembly affect host fitness in Daphnia

AbstractThe arrival order of species can strongly influence the early assembly of ecological communities. Such events, known as priority effects, are documented in various ecological settings, but remain understudied within the context of the gut microbiome. Given the fundamental link between the gut microbiome and host health, exploring the potential role of priority effects in shaping the assembly and development of microbial communities within the gut becomes imperative. Using the freshwater planktonic crustacean Daphnia magna as a model system, we manipulated the immigration order of three bacterial strain pairs in two germ‐free genotypes and quantified gut microbiome composition and host fitness at two time points, namely day 8 and day 12. Priority effects were observed; however, their presence, amplitude, and direction (suppressive or facilitative) were found to be contingent on the identity of bacterial strain and host genotype. These findings were accompanied by notable differences in Daphnia life history traits across inoculation order treatments, shedding light on the tangible consequences of priority effects triggered by the sequence of bacterial strain arrival in the gut environment, for host fitness. Our results thus highlight the complex nature of priority effects in gut community assembly, their strain/genotype specificity, and their potential impact on the host.

Strain‐dependent and host genotype–dependent priority effects in gut microbiome assembly affect host fitness in Daphnia

AbstractThe arrival order of species can strongly influence the early assembly of ecological communities. Such events, known as priority effects, are documented in various ecological settings, but remain understudied within the context of the gut microbiome. Given the fundamental link between the gut microbiome and host health, exploring the potential role of priority effects in shaping the assembly and development of microbial communities within the gut becomes imperative. Using the freshwater planktonic crustacean Daphnia magna as a model system, we manipulated the immigration order of three bacterial strain pairs in two germ‐free genotypes and quantified gut microbiome composition and host fitness at two time points, namely day 8 and day 12. Priority effects were observed; however, their presence, amplitude, and direction (suppressive or facilitative) were found to be contingent on the identity of bacterial strain and host genotype. These findings were accompanied by notable differences in Daphnia life history traits across inoculation order treatments, shedding light on the tangible consequences of priority effects triggered by the sequence of bacterial strain arrival in the gut environment, for host fitness. Our results thus highlight the complex nature of priority effects in gut community assembly, their strain/genotype specificity, and their potential impact on the host.

The microbiota characterizing huge carbonatic moonmilk structures and its correlation with preserved organic matter

BackgroundMoonmilk represents complex secondary structures and model systems to investigate the interaction between microorganisms and carbonatic rocks. Grotta Nera is characterized by numerous moonmilk speleothems of exceptional size hanging from the ceiling, reaching over two meters in length. In this work we combined microbiological analyses with analytical pyrolysis and carbon stable isotope data to determine the molecular composition of these complex moonmilk structures as well as the composition of the associated microbiota.ResultsThree moonmilk structures were dissected into the apical, lateral, and core parts, which shared similar values of microbial abundance, richness, and carbon isotopes but different water content, microbiota composition, and organic matter. Moonmilk parts/niches showed higher values of microbial biomass and biodiversity compared to the bedrock (not showing moonmilk development signs) and the waters (collected below dripping moonmilk), indicating the presence of more complex microbial communities linked to carbonate rock interactions and biomineralization processes. Although each moonmilk niche was characterized by a specific microbiota as well as a distinct organic carbon profile, statistical analyses clustered the samples in two main groups, one including the moonmilk lateral part and the bedrock and the other including the core and apical parts of the speleothem. The organic matter profile of both these groups showed two well-differentiated organic carbon groups, one from cave microbial activity and the other from the leaching of vascular plant litter above the cave. Correlation between organic matter composition and microbial taxa in the different moonmilk niches were found, linking the presence of condensed organic compounds in the apical part with the orders Nitrospirales and Nitrosopumilales, while different taxa were correlated with aromatic, lignin, and polysaccharides in the moonmilk core. These findings are in line with the metabolic potential of these microbial taxa suggesting how the molecular composition of the preserved organic matter drives the microbiota colonizing the different moonmilk niches. Furthermore, distinct bacterial and archaeal taxa known to be involved in the metabolism of inorganic nitrogen and C1 gases (CO2 and CH4) (Nitrospira, Nitrosopumilaceae, Nitrosomonadaceae, Nitrosococcaceae, and novel taxa of Methylomirabilota and Methanomassiliicoccales) were enriched in the core and apical parts of the moonmilk, probably in association with their contribution to biogeochemical cycles in Grotta Nera ecosystem and moonmilk development.ConclusionsThe moonmilk deposits can be divided into diverse niches following oxygen and water gradients, which are characterized by specific microbial taxa and organic matter composition originating from microbial activities or deriving from soil and vegetation above the cave. The metabolic capacities allowing the biodegradation of complex polymers from the vegetation above the cave and the use of inorganic nitrogen and atmospheric gases might have fueled the development of complex microbial communities that, by interacting with the carbonatic rock, led to the formation of these massive moonmilk speleothems in Grotta Nera.

Compost and Beneficial Pseudomonas Populations Promote Enzyme Activity, Amino Acids and Polymers Utilization Patterns in Heavy Metal Contaminated Soils

PGPR-assisted phytoremediation is a biotechnology offering opportunities to improve the state of contaminated soil ecosystems. The present study has investigated the potential of six beneficial isolates tolerant to Cd, Pb, and Zn and identified through 16S rDNA sequential analysis as Bacillus cereus, Pseudomonas putida, and Pseudomonas fluorescens to stimulate spinach growth and soil microbial community development in heavy metal-contaminated soil with or without the addition of compost. We found improved plant growth in all treatments with compost, but especially applying consortiums of isolates. Microbial enzyme activities and basal soil respiration were significantly higher in the rhizosphere and in amended treatments than in non-rhizosphere and control. The microbial community-level physiological profiles in the rhizosphere studied with the Ecoplates of BiologTM system showed increased metabolic potential in treatments with compost and beneficial bacteria. Principal component analysis revealed domination of amino acids and polymers utilizing communities in compost and bacterial consortium amended soils, carbohydrates and amino acids in compost and single strains application, and the lowest representation of amines and amides and phenolic compounds utilizers. Thus, may conclude that the use of quality organic amendments together with beneficial soil bacterial populations is a suitable and promising approach for the phytostabilization of soils contaminated with heavy metals.

Pediococcus spp.-mediated competition interaction within Daqu microbiota determines the temperature formation and metabolic profiles.

Fermented microbiota is critical to the formation of microenvironment and metabolic profiles in spontaneous fermentation. Microorganisms generate a diverse array of metabolites concurrent with the release of heat energy. In the case of Daqu fermentation, the peak temperature exceeded 60°C, forming a typical high-temperature fermentation system known as high-temperature Daqu. However, microorganisms that cause the quality variation in Daqu and how they affect the functional microbiota and microenvironment in the fermentation process are not yet clear. This study adopted high-throughput sequencing and monitored the dynamic fluctuations of metabolites and environmental factors to identify the pivotal microorganism responsible for the alterations in interaction patterns of functional keystone taxa and quality decline in the fermentation system of different operational areas during the in situ fermentation process that had been mainly attributed to operational taxonomic unit (OTU)_22 (Pediococcus acidilactici). Additionally, we used isothermal microcalorimetry, plate inhibition experiments, and in vitro simulation fermentation experiments to explore the impact of Pediococcus spp. on heat generation, microorganisms, and metabolite profiles. Results showed the heat peak generated by Pediococcus spp. was significantly lower than that of Bacillus spp., filamentous fungi, and yeast. In addition, the preferential growth of P. acidilactici strain AA3 would obviously affect other strains to colonize through competition, and its metabolites made a significant impact on filamentous fungi. The addition of P. acidilactici strain AA3 in simulated fermentation would cause the loss of pyrazines and acids in metabolites. These evidences showed that the overgrowth of Pediococcus spp. greatly influenced the formation of high temperatures and compounds in solid-state fermentation systems. Our work illustrated the vital impact of interaction variability mediated by Pediococcus spp. for microbial assembly and metabolites, as well as in forming temperature. These results emphasized the functional role of Daqu microbiota in metabolites and heat production and the importance of cooperation in improving the fermentation quality.IMPORTANCEThe stable and high-quality saccharifying and fermenting starter in traditional solid-state fermentation was the prerequisite for liquor brewing. An imbalance of microbial homeostasis in fermentation can adversely impact production quality. Identification of such critical microorganisms and verifying their associations with other fermentation parameters pose a challenge in a traditional fermentation environment. To enhance the quality of spontaneous fermented products, strategies such as bioaugmentation or the control of harmful microorganisms would be employed. This work started with the differences in high-temperature Daqu metabolites to explore a series of functional microorganisms that could potentially contribute to product disparities, and found that the differences in interactions facilitated directly or indirectly by Pediococcus spp. seriously affected the development of microbial communities and metabolites, as well as the formation of the microenvironment. This study not only identified functional microbiota in Daqu that affected fermentation quality, but also demonstrated how microorganisms interact to affect the fermentation system, which would provide guidance for microbial supervision in the actual production process. Besides, the application of isothermal microcalorimetry in this study was helpful for us to understand the heat production capacity of microorganisms and their adaptability to the environment. This study presented a commendable framework for improving and controlling the quality of traditional fermentation and inspired further investigations in similar systems.

Microbial community evolution and individual-based model validation of biofilms in single-stage partial nitrification/anammox system

In this study, matrix degradation, microbial community development, and distribution using an individual-based model during biofilm formation on carriers at varying depths within a single-stage partial nitrification/anammox system were simulated. The findings from the application of individual-based model fitting, fluorescence in situ hybridization, and high-throughput sequencing reveal the presence of aerobic bacteria, specifically ammonia-oxidizing bacteria, as discrete particles within the outer layer of the carrier. Facultative anaerobic bacteria exemplified by anaerobic ammonia-oxidizing bacteria, are observed as aggregates within the middle layer. Conversely, anaerobic bacteria, represented by denitrifiers, are enveloped by extracellular polymeric substances within the inner layer. The present study extends the application of individual-based model to the formation of polyurethane-supported biofilms and presents valuable avenues for the design and advancement of pragmatic engineering carriers.

Study on the effect of compound cultivation on the growth feature and active ingredients content of Salvia miltiorrhiza.

We investigated the effects of the complex cultivation of Salvia miltiorrhiza on microbial communities, secretions, yield, and active ingredients, and the mechanism of action between microbial communities, secretions, and S. miltiorrhiza growth and development. Neither maize nor soybean was suitable to grow with S. miltiorrhiza, but sesame significantly increased salvinone content, the active ingredient of S. miltiorrhiza, and Tanshinone IIA, Tanshinone I, and Cryptotanshinone increased by 27.06%, 22.76%, and 26.41%, respectively, which increased the abundance and number of microbial communities in S. miltiorrhiza roots. 16S rRNA results showed that the most abundant bacterial phyla were Proteobacteria and Acidobacteriota, and their number increased with compound planting of sesame and S. miltiorrhiza. Salvia inter-root secretions affected the microbial community and Salvia growth and development, and lipids and lipid-like molecules significantly reduced Salvia yield and active ingredients. Overall, different plant secretions can lead to differences in the natural environment and Salvia root growth and development, and the composite planting of sesame with Salvia can improve inter-root microbial communities, enhance Salvia quality, and make fuller use of land resources.

Weaning transition, but not the administration of probiotic candidate Kazachstania slooffiae, shaped the gastrointestinal bacterial and fungal communities in nursery piglets.

As in-feed antibiotics are phased out of swine production, producers are seeking alternatives to facilitate improvements in growth typically seen from this previously common feed additive. Kazachstania slooffiae is a prominent commensal fungus in the swine gut that peaks in relative abundance shortly after weaning and has beneficial interactions with other bacteriome members important for piglet health. In this study, piglets were supplemented with K. slooffiae to characterize responses in piglet health as well as fungal and bacterial components of the microbiome both spatially (along the entire gastrointestinal tract and feces) and temporally (before, during, and after weaning). Litters were assigned to one of four treatments: no K. slooffiae (CONT); one dose of K. slooffiae 7 days before weaning (day 14; PRE); one dose of K. slooffiae at weaning (day 21; POST); or one dose of K. slooffiae 7 days before weaning and one dose at weaning (PREPOST). The bacteriome and mycobiome were analyzed from fecal samples collected from all piglets at day 14, day 21, and day 49, and from organ samples along the gastrointestinal (GI) tract at day 21 and day 49. Blood samples were taken at day 14 and day 49 for cytokine analysis, and fecal samples were assayed for antimicrobial resistance. While some regional shifts were seen in response to K. slooffiae administration in the mycobiome of the GI tract, no remarkable changes in weight gain or health of the animals were observed, and changes were more likely due to sow and the environment. Ultimately, the combined microbiome changed most considerably following the transition from suckling to nursery diets. This work describes the mycobiome along the piglet GI tract through the weaning transition for the first time. Based on these findings, K. slooffiae administered at this concentration may not be an effective tool to hasten colonization of K. slooffiae in the piglet GI tract around the weaning transition nor support piglet growth, microbial gut health, or immunity. However, diet and environment greatly influence microbial community development.

Seafloor incubation experiments at deep-sea hydrothermal vents reveal distinct biogeographic signatures of autotrophic communities.

The discharge of hydrothermal vents on the seafloor provides energy sources for dynamic and productive ecosystems, which are supported by chemosynthetic microbial populations. These populations use the energy gained by oxidizing the reduced chemicals contained within the vent fluids to fix carbon and support multiple trophic levels. Hydrothermal discharge is ephemeral and chemical composition of such fluids varies over space and time, which can result in geographically distinct microbial communities. To investigate the foundational members of the community, microbial growth chambers were placed within the hydrothermal discharge at Axial Seamount (Juan de Fuca Ridge), Magic Mountain Seamount (Explorer Ridge), and Kama'ehuakanaloa Seamount (Hawai'i hotspot). Campylobacteria were identified within the nascent communities, but different amplicon sequence variants were present at Axial and Kama'ehuakanaloa Seamounts, indicating that geography in addition to the composition of the vent effluent influences microbial community development. Across these vent locations, dissolved iron concentration was the strongest driver of community structure. These results provide insights into nascent microbial community structure and shed light on the development of diverse lithotrophic communities at hydrothermal vents.

Impact of salinity and time on structure and functional potential of wastewater treatment biofilms in intermittent sand bioreactors.

High salt wastewater is produced in industries, including seafood and pickling processing. The salinity in such wastewaters has been shown to negatively impact biological treatment efficacy. Little is known about the changes in the microbial community structure in the mature biological treatment systems, the impacts of salinity on community composition, and the shifts over time during operation. Specifically, intermittent sand bioreactors (ISBs) with a focus on ammonia treatment were utilized. This study aimed to identify the changes in the microbial community due to both salt and days of operation through 16s rRNA sequencing and KEGG functional predictions. Results showed that the overall community structure and diversity were distinct as wastewater salinity varied from 0%-1.3%. At 1.3% salinity Zoogloea, a common genus in wastewater treatment plants, was not present and Aequorovita, Thaura and Dokdonella became the dominant genera. Nitrosomonas, an important ammonia oxidizing bacteria, increased in abundance with days of operation but was not significantly impacted by an increase in salinity. This finding was further supported by an increase in predicted nitrification potential with time of operation within all intermittent sand bioreactors tested. These results provide a deeper understanding of the impacts of salinity on microbial community development in biological treatment systems and elucidate the shifts in community structure occurring during early operations and into system maturity.

In vitro fermentation of substrates from Saccharina latissima by broiler chicken’s caecal microbiota

This study investigated seasonal variations in the composition of the kelp species Saccharina latissima cultivated on the Swedish west coast and, using an in vitro fermentation system, evaluated the effect of fermented whole S. latissima biomass or biomass components on the gut microbiota of broiler chickens. Caecal contents of six Ross 308 broilers fed a standard wheat and soy-based diet were retrieved on two different occasions, with three birds sampled per occasion. Two in vitro fermentation batches (A, B) were established using caecal contents as inoculum, and whole S. latissima, ethanol-washed S. latissima, laminarin extract or inulin (control) as substrate. Total short-chain fatty acid (SCFA) content, gas production, pH and changes in microbiota composition were studied after 6, 12 and 24 h of fermentation. Analysis of seasonal variations revealed that S. latissima harvested in June had the highest laminarin content and lowest ash and crude protein content. Broiler microbiota, SCFA profile, gas production and pH mainly varied depending on fermentation inoculum, but there were also some variations depending on substrate. For instance, uncultured bacterium from Clostridiales_vadinBB60_group showed higher relative abundance (RA) in batch A, while Faecalibacterium showed higher RA in batch B. Whole and ethanol-washed S. latissima resulted in highest RA of unclassified Ruminococcaceae and Tyzzerella for both batches, while ethanol-washed S. latissima and laminarin gave highest RA of Erysipelatoclostridium. Inulin resulted in highest RA for the genus Subdoligranulum. Acetic, n-butyric and propionic acid were the main fermentation products and total SCFA level was higher in batch B. Within batch B, inulin and laminarin generated higher levels of acetic and butyric acid. When using inulin and laminarin, gas production was lower in batch B compared with batch A. In summary, this study showed that S. latissima is a good source of laminarin, especially when harvested in summer. Within the in vitro system, the microbiota was affected by different substrates, but inoculum source was identified as an important contributor to microbial community development during fermentation.

Spatio-temporal distribution characteristics and influencing factors of protoporphyrin IX in the estuarine-coastal ecosystems

Protoporphyrin IX (PPIX), a key precursor for the synthesis of chlorophyll and heme, is fundamental to photosynthetic eukaryotic cells and participates in light absorption, energy transduction, and numerous other cellular metabolic activities. Along with the application of genetic and biochemical techniques over the past few years, our understanding of the formation of PPIX has been largely advanced, especially regarding possible metabolic pathways. However, the ecological role and function of PPIX in natural ecosystems remains unclear. We have previously established a method for quantifying PPIX in marine ecosystems. Here, our results provide evidence that PPIX is not only subtly linked to nutrient uptake but also triggers phytoplankton productivity. PPIX and its derivatives are dynamic spatiotemporally in direct response to increased nutrient availability. Using 16 S rRNA gene amplicon sequencing, PPIX was revealed to interact strongly with many microorganisms, indicating that PPIX serves as a critical metabolite in maintaining microbial metabolism and community development. In summary, we observed that PPIX is linearly related to nutrient availability and microbial diversity. The levels of microbial PPIX reflect ecological health, and the availability of PPIX and nutrients jointly affect microbial community composition.

Effect of organic amendments on soil structure, microbial community and water transport in the Qinghai Lake watershed, North-Eastern Qinghai–Tibet Plateau

ABSTRACT The effect of organic amendments on soil structure, microbial community and water transport in alpine ecosystems remains uncertain. Six fertilization regimes from a 2-year field experiment were selected to study this mechanism, i.e. plant litter (PL), organic fertilizer (OF), low concentration of glucose (LCG), medium concentration of glucose (MCG), high concentration of glucose (HCG) and the control (CT). Our results indicated that the soil macroporosity, branch density, length density and node density of soil macropores treated with OF, PL, HCG, MCG and LCG were larger than those of soils treated with CT. The phospholipid fatty acids (PLFAs), bacteria, fungi, actinomycetes, gram-positive bacteria (G+) and gram-negative bacteria (G−) of soils treated with OF, PL, HCG and MCG were larger than those of soils treated with LCG and CT. In contrast, the dyed area ratio and the maximum wetting depth of soils treated with OF, PL, LCG, HCG and MCG were smaller than those treated with CT. There were significant positive correlations between soil organic matter (SOM) and connectivity of soil macropores. Therefore, SOM accumulation significantly improved the soil pore structure, induced the development of the soil microbial community, increased the soil water retention ability and decreased the generation of preferential flow.

Gut microbiota changes in Hexagrammos otakii during development and association with diets based on metagenomics sequencing

The development of microbial communities is important for the growth of the fat greenling Hexagrammos otakii; however, the relationship between microbial communities and fish diet is poorly understood. Here, we used metagenomics sequencing to investigate the gut microbiota of H. otakii at three key time points during development. The gut microbial diversity and community composition of H. otakii presented stage-specific signatures and appeared to shift with different diets and environmental conditions such as NH4 + -NO2- etc. Metagenomics analysis indicated that the dominant phyla were Proteobacteria and Firmicutes. With dietary changes from rotifers and Artemia to formulated feed, the dominant genera shifted from Vibrio and Photobacterium to Lactococcus, and variations in the gut microbiota increased with age. Based on metagenomics functional annotation using the Kyoto Encyclopedia of Genes and Genomes database, growth and diet at different stages affected the metabolic function of the gut microbiome by activating carbohydrate and amino acid metabolism while weakening lipid and nucleotide metabolism. In addition, as predicted by the Carbohydrate-Active enZymes database, glycoside hydrolase and glycosyl transferases may be involved in food degradation. Our results suggest that the H. otakii gut microbiota assembly was coupled to animal development and host age-associated biotic features and changes. Diet had a considerable effect on these distinct communities at different times, indicating that the fish gut microbiota rapidly adapted to dietary shifts. The microbiota therefore likely plays an indispensable role in nutrient turnover and fermentation. These findings can provide guidance for the development of probiotics and the application of feed additives.

Influence of Hydrodynamic Forces on Electroactive Bacterial Adhesion in Microbial Fuel Cell Anodes.

This investigation examined the role of shear stress on the dynamic development of microbial communities within anodic biofilms in single-chamber microbial fuel cells (MFCs). Bacterial attachment to surfaces, often regarded as a crucial step in biofilm formation, may significantly contribute to the selection of electroactive bacteria (EAB). It is well established that hydrodynamic forces, particularly shear forces, have a profound influence on bacterial adhesion. This study postulates that shear stress could select EAB on the anode during the adhesion phase by detaching non-EAB. To examine this hypothesis, MFC reactors equipped with a shear stress chamber were constructed, creating specific shear stress on the anode. The progression of adhesion under various shear stress conditions (1, 10, and 50 mPa) was compared with a control MFC lacking shear stress. The structure of the microbial community was assessed using 16S rRNA gene (rrs) sequencing, and the percentage of biofilm coverage was analyzed using fluorescence microscopy. The results indicate a significant impact of shear stress on the relative abundance of specific EAB, such as Geobacter, which was higher (up to 30%) under high shear stress than under low shear stress (1%). Furthermore, it was noted that shear stress decreased the percentage of biofilm coverage on the anodic surface, suggesting that the increase in the relative abundance of specific EAB occurs through the detachment of other bacteria. These results offer insights into bacterial competition during biofilm formation and propose that shear stress could be utilized to select specific EAB to enhance the electroactivity of anodic biofilms. However, additional investigations are warranted to further explore the effects of shear stress on mature biofilms.

Simultaneous spatiotemporal transcriptomics and microscopy of Bacillus subtilis swarm development reveal cooperation across generations.

Development of microbial communities is a complex multiscale phenomenon with wide-ranging biomedical and ecological implications. How biological and physical processes determine emergent spatial structures in microbial communities remains poorly understood due to a lack of simultaneous measurements of gene expression and cellular behaviour in space and time. Here we combined live-cell microscopy with a robotic arm for spatiotemporal sampling, which enabled us to simultaneously acquire phenotypic imaging data and spatiotemporal transcriptomes during Bacillus subtilis swarm development. Quantitative characterization of the spatiotemporal gene expression patterns revealed correlations with cellular and collective properties, and phenotypic subpopulations. By integrating these data with spatiotemporal metabolome measurements, we discovered a spatiotemporal cross-feeding mechanism fuelling swarm development: during their migration, earlier generations deposit metabolites which are consumed by later generations that swarm across the same location. These results highlight the importance of spatiotemporal effects during the emergence of phenotypic subpopulations and their interactions in bacterial communities.

Effects of granular feed on reproductive metabolism of breeding pigeons, intestinal development and microbiota of squab pigeons–A double-edged sword

Pigeons like to eat raw grains, but meat pigeon enterprises often use compound feeds instead of raw grains to feed breeding pigeons to increase economic efficiency, which may change the pigeon's dietary behavior, and consequently lead to health and welfare problems. The purpose of this study was to investigate the effect of granular feeds on the health of high-yielding breeding pigeons and squabs in lactation. The results showed that, compared with raw grain group, the provision of granular feed resulted in lower total feed intake without affecting the weight of lactating breeding pigeons. Meanwhile, reproductive metabolism was improved and no oxidative stress was observed, which indicated that granular feeds had a positive effect on breeding pigeon's health. However, granular feed adversely affected jejunum development in squabs, compare wtih raw grain group, the growth rate of squab was reduced. Sequencing of the 16 s rRNA gene revealed that granular feed induced intestinal microbiota dysbiosis in the squabs. The use of granular feed reduced the relative abundance of gut microorganisms in functional categories related to lipid and energy metabolism, resulting in a decrease in the relative abundance of beneficial bacteria such as Bifidobacterium, Ligilactobacillus, Atopobium, and an increase in that of inflammation-related Limosilactobacillus, which likely inhibited squab intestinal development and growth. Although the use of granular feed can improve breeder metabolism, it affect the composition of the microbial community and gut development of squabs. Therefore, the use of granular feed in production should be more careful to avoid causing growth obstruction of squab.

Effects of Fe(III) (hydr)oxide mineralogy on the development of microbial communities originating from soil, surface water, groundwater, and aerosols

Microbial Fe(III) reduction is a key component of the iron cycle in natural environments. However, the susceptibility of Fe(III) (hydr)oxides to microbial reduction varies depending on the mineral's crystallinity, and the type of Fe(III) (hydr)oxide in turn will affect the composition of the microbial community. We created microcosm reactors with microbial communities from four different sources (soil, surface water, groundwater, and aerosols), three Fe(III) (hydr)oxides (lepidocrocite, goethite, and hematite) as electron acceptors, and acetate as an electron donor to investigate the shaping effect of Fe(III) mineral type on the development of microbial communities. During a 10-month incubation, changes in microbial community composition, Fe(III) reduction, and acetate utilization were monitored. Overall, there was greater reduction of lepidocrocite than of goethite and hematite, and the development of microbial communities originating from the same source diverged when supplied with different Fe(III) (hydr)oxides. Furthermore, each Fe(III) mineral was associated with unique taxa that emerged from different sources. This study illustrates the taxonomic diversity of Fe(III)-reducing microbes from a broad range of natural environments.