Changes In Microbial Community Composition Research Articles

Effects of Variation in Tamarix chinensis Plantations on Soil Microbial Community Composition in the Middle Yellow River Floodplain

Floodplains have important ecological and hydrological functions in terrestrial ecosystems, experience severe soil erosion, and are vulnerable to losing soil fertility. Tamarix chinensis Lour. plantation is the main vegetation restoration measure for maintaining soil quality in floodplains. Soil microorganisms are essential for driving biogeochemical cycling processes. However, the effects of sampling location and shrub patch size on soil microbial community composition remain unclear. In this study, we characterized changes in microbial structure, as well as the factors driving them, in inside- and outside-canopy soils of three patch sizes (small, medium, large) of T. chinensis plants in the middle Yellow River floodplain. Compared with the outside-canopy soils, inside-canopy had higher microbial phospholipid fatty acids (PLFAs), including fungi, bacteria, Gram-positive bacteria (GP), Gram-negative bacteria (GN), and arbuscular mycorrhizal fungi. The ratio of fungi to bacteria and GP to GN gradually decreased as shrub patch size increased. Differences between inside-canopy and outside-canopy soils in soil nutrients (organic matter, total nitrogen, and available phosphorus) and soil salt content increased by 59.73%, 40.75%, 34.41%, and 110.08% from small to large shrub patch size. Changes in microbial community composition were mainly driven by variation in soil organic matter, which accounted for 61.90% of the variation in inside-canopy soils. Resource islands could alter microbial community structure, and this effect was stronger when shrub patch size was large. The results indicated that T. chinensis plantations enhanced the soil nutrient contents (organic matter, total nitrogen, and available phosphorus) and elevated soil microbial biomass and changed microbial community composition; T. chinensis plantations might thus provide a suitable approach for restoring degraded floodplain ecosystems.

Dynamic changes of microbial community composition and diversity in metal contaminated and reclaimed lands assessed by Illumina MiSeq sequencing

Dynamic changes of microbial community composition and diversity in metal contaminated and reclaimed lands assessed by Illumina MiSeq sequencing

Adaptation of Rhizosphere Microbial Communities to Continuous Exposure to Multiple Residual Antibiotics in Vegetable Farms.

The constant application of manure-based fertilizers in vegetable farms leads to antibiotic residue accumulation in soils, which has become a major stressor affecting agroecosystem stability. The present study investigated the adaptation profiles of rhizosphere microbial communities in different vegetable farms to multiple residual antibiotics. Multiple antibiotics, including trimethoprim, sulfonamides, quinolones, tetracyclines, macrolides, lincomycins, and chloramphenicols, were detected in the vegetable farms; the dominant antibiotic (trimethoprim) had a maximum concentration of 36.7 ng/g. Quinolones and tetracyclines were the most prevalent antibiotics in the vegetable farms. The five most abundant phyla in soil samples were Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi and Firmicutes, while the five most abundant phyla in root samples were Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Myxococcota. Macrolides were significantly correlated with microbial community composition changes in soil samples, while sulfonamides were significantly correlated with microbial community composition changes in root samples. Soil properties (total carbon and nitrogen contents and pH) influenced the shifts in microbial communities in rhizosphere soils and roots. This study provides evidence that low residual antibiotic levels in vegetable farms can shift microbial community structures, potentially affecting agroecosystem stability. However, the degree to which the shift occurs could be regulated by environmental factors, such as soil nutrient conditions.

Different types of land use influence soil physiochemical properties, the abundance of nitrifying bacteria, and microbial interactions in tropical urban soil

Anthropogenic activities have led to unexpected changes in microbial community composition and structure, resulting in an interruption of soil ecological roles in urban environments. We questioned the impact of the different land use (e.g., agricultural, industrial, recreational, coastal, and residential areas) on the distribution of nitrifying bacteria and microbial interaction in tropical soil. The dominant nitrifying bacteria were ammonia-oxidizing archaea (AOA) in tropical soils up to 107 copies/g of soil, while the abundance of ammonia-oxidizing bacteria (AOB) was significantly higher in agricultural soil only. Comammox (CMX) was ubiquitous up to 105 copies/g of tropical soil, indicating that CMX might share ecological niches with AOA and considerably contribute to nitrification in urban areas. The most abundant phylum is Actinobacteria, accounting for 27–34 % relative abundance among most land-use types, but Proteobacteria was observed as the most prevalent phylum in agricultural soil. The physicochemical properties (e.g., soil pH and nutrient contents) of different types of land use influenced microbial richness and diversities associated with nitrogen cycling. Multivariate analysis disclosed that agricultural soils were distinct from other land uses because of the concentrations of nutrients and heavy metals and the abundance of microorganisms associated with nitrogen cycles. Also, the microbial co-occurrence network revealed that agricultural soils were a highly interconnected network of the microbial community. In this study, C: N ratio might have a significant impact on ecological networks and the abundance of nitrogen-related taxa, which could influence microbial interactions and complexity in tropical soils. Thus, the impact of anthropogenic land use induced changes in microbial composition and diversity, co-occurrence network, and nitrifying bacteria, leading to potential transformation in ecological services of tropical soils and nitrogen cycling in urban environments.

Altered gastrointestinal tract structure and microbiome following cerebral malaria infection.

Cerebral malaria (CM) is the most severe form of malaria with the highest mortality rate and can result in life-long neurological deficits and ongoing comorbidities. Factors contributing to severity of infection and development of CM are not fully elucidated. Recent studies have indicated a key role of the gut microbiome in a range of health conditions that affect the brain, but limited microbiome research has been conducted in the context of malaria. To address this knowledge gap, the impact of CM on the gut microbiome was investigated in mice. C57BL/6J mice were infected with Plasmodium berghei ANKA (PbA) parasites and compared to non-infected controls. Microbial DNA from faecal pellets collected daily for 6-days post-infection were extracted, and microbiome comparisons conducted using 16S rRNA profiling. We identified significant differences in the composition of bacterial communities between the infected and the non-infected groups, including a higher abundance of the genera Akkermansia, Alistipes and Alloprevotella in PbA-infected mice. Furthermore, intestinal samples were collected post-cull for morphological analysis. We determined that the caecal weight was significantly lower, and the small intestine wassignificantly longer in PbA-infected mice than in the non-infected controls. We concluded that changes in microbial community composition were primarily driven by the infection protocol and, to a lesser extent, by the time of infection. Our findings pave the way for a new area of research and novel intervention strategies to modulate the severity of cerebral malaria disease.

Depth-related patterns in microbial community responses to complex organic matter in the western North Atlantic Ocean

Abstract. Oceanic bacterial communities process a major fraction of marine organic carbon. A substantial portion of this carbon transformation occurs in the mesopelagic zone, and a further fraction fuels bacteria in the bathypelagic zone. However, the capabilities and limitations of the diverse microbial communities at these depths to degrade high-molecular-weight (HMW) organic matter are not well constrained. Here, we compared the responses of distinct microbial communities from North Atlantic epipelagic (0–200 m), mesopelagic (200–1000 m), and bathypelagic (1000–4000 m) waters at two open-ocean stations to the same input of diatom-derived HMW particulate and dissolved organic matter. Microbial community composition and functional responses to the input of HMW organic matter – as measured by polysaccharide hydrolase, glucosidase, and peptidase activities – were very similar between the stations, which were separated by 1370 km but showed distinct patterns with depth. Changes in microbial community composition coincided with changes in enzymatic activities: as bacterial community composition changed in response to the addition of HMW organic matter, the rate and spectrum of enzymatic activities increased. In epipelagic mesocosms, the spectrum of peptidase activities became especially broad and glucosidase activities were very high, a pattern not seen at other depths, which, in contrast, were dominated by leucine aminopeptidase and had much lower peptidase and glucosidase rates in general. The spectrum of polysaccharide hydrolase activities was enhanced particularly in epipelagic and mesopelagic mesocosms, with fewer enhancements in rates or spectrum in bathypelagic waters. The timing and magnitude of these distinct functional responses to the same HMW organic matter varied with depth. Our results highlight the importance of residence times at specific depths in determining the nature and quantity of organic matter reaching the deep sea.

Evaluation of Anaerobic Soil Disinfestation for Environmentally Sustainable Weed Management

In anaerobic soil disinfestation (ASD), soil amended with a carbon source undergoes anaerobic conditions accompanied by changes in microbial community composition and an increase in the concentration of organic acids, primarily acetic and butyric acids, and gases that are deleterious to plant pathogens, insects, and potentially to weeds. The purpose of this study was to explore the efficacy of ASD with different carbon sources on inactivation of propagules of a variety of weed species. Germination and viability of propagules of common lambsquarters (Chenopodium album L.), black nightshade (Solanum nigrum L.), yellow nutsedge (Cyperus esculentus L.), common pokeweed (Phytolacca decandra L.), barnyardgrass (Echinochloa crus-galli L.), dandelion (Taraxacum officinale (Weber)), and redroot pigweed (Amaranthus retroflexus L.) were tested using different rates of four carbon sources: molasses, wheat bran, mustard greens biomass, and raw chicken manure. Wheat bran was the most effective carbon source for inactivation of all weed propagules, followed by molasses and mustard greens biomass. Carbon sources were mixed with soil, which was irrigated to saturation and covered with plastic to promote anaerobic conditions for three weeks. Chicken manure inactivated all the tested species except A. retroflexus compared to the anaerobic control. Rates of carbon sources applied in soil were weakly but significantly correlated (r > 0.42 and p < 0.04) with weed seed mortality or germination inhibition (E. crus-galli) for all the tested carbon sources and weed species except for chicken manure for C. album, A. retroflexus, and S. nigrum. Laboratory tests to confirm organic acid toxicity showed that 1000 µL L−1 acetic plus 1000 µL L−1 butyric acids for at least 60 h inhibited of sprouting of C. esculentus tubers and E. crusgalli seeds, whereas 120 h or exposure was required to inhibit C. album seed germination. Anaerobic soil disinfestation effectively suppressed weed seed germination and viability when wheat bran, molasses and mustard greens biomass were used as carbon sources. This approach could be adopted for weed management in organic systems or any farming system where priority is given to environmentally sustainable practices.

Divergent responses in the gut microbiome and liver metabolome to ammonia stress in three freshwater turtles

Ammonia is a common pollutant in aquaculture system, and toxic to all aquatic animals. However, different aquatic animals exhibit diverse physiological responses to high-level ammonia exposure, potentially indicating their divergent resistance to ammonia stress. In this study, juveniles of three freshwater turtles (Mauremys reevesii, Pseudemys nelsoni and Trachemys scripta elegans) were exposed to different concentrations of ammonia (0, 0.3 and 3.0 mg/L) for 30 days, and their swimming, growth performance, gut microbiota, and hepatic metabolites were measured to evaluate the interspecific difference in physiological responses to ammonia stress. Despite no differences in swimming ability, growth rate, and gut microbial diversity, observable changes in microbial community composition and hepatic metabolite profiles were shown in ammonia-exposed turtles. A relatively higher abundance of potentially pathogenic bacteria was found in M. reevesii than in the other two species. Moreover, microbial compositions and metabolic responses differed significantly among the three species. M. reevesii was, out of the three tested species, the one in which exposure to ammonia had the greatest effect on changes in bacterial genera and hepatic metabolites. Conversely, only a few metabolites were significantly changed in T. scripta elegans. Integrating these findings, we speculated that native M. reevesii should be more vulnerable to ammonia stress compared to the invasive turtle species. Our results plausibly reflected divergent potential resistance to ammonia among these turtles, in view of differential physiological responses to ammonia exposure at environmentally relevant concentrations.

Immunomodulatory Microbial Metabolites Identified in Allo-SCT Patients Protect from GvHD By Sting Dependent Modulation of Intestinal Tissue Homeostasis

Background: Graft-versus-host disease (GVHD) is a dreaded complication after allogeneic stem-cell transplantation (ASCT). Previously, we and others showed that activation of type I interferon (IFN-I) inducing pathways such as RIG-I/MAVS or cGAS/STING can promote the integrity of the intestinal barrier and limit GVHD. However, the signals that drive these protective IFN-I responses are poorly understood. Commensal microbiota can (i) have distant effects on immune responses through modulation of IFN-I signaling and (ii) predict mortality in ASCT patients. We hypothesized that microbiota-derived products such as microbial metabolites engage IFN-I signaling in immune and non-immune cells poising them for induction of protective responses. We established a prospective, multi-centric clinical study in patients newly diagnosed with acute leukemia and performed longitudinal stool sampling to track changes in microbial community composition and metabolites expression levels (Submitted as a separate abstract to ASH 2022 (Orberg & Meedt et al.)). We showed that patients with high metabolite expression are less likely to develop GVHD. In this study, we translated our clinical observations to mouse models of acute GVHD and human and mouse intestinal organoid models to uncover the molecular mechanisms of protective metabolites during ASCT. Methods: Stool samples from ASCT patients were obtained in Munich and Regensburg in accordance to IRB-approved study protocols. Patients were sampled at initial diagnosis (Dx), prior to conditioning and weekly after ASCT up to day 28. We analyzed samples by 16S rRNA sequencing and mass spectrometry. Next, we tested metabolites detected in patients in vitro in murine and human intestinal crypt-derived organoids and organoid/T cell coculture assays. To obtain a mechanistic understanding, we stimulated WT or IFN-I-signaling-impaired organoids or used small molecule inhibitors and analysed them regarding growth performance, cell composition and by scRNAseq. Finally, Metabolites were applied as treatment in preclinical intestinal damage models and GVHD mouse models. Outcomes were assessed by a novel organoid recovery assay in addition to established read-outs. Results: Here, we present expression profiles of metabolites including short-chain fatty acids, DAT, ICA and secondary bile acids. Following ASCT, and especially at the early time-points, metabolite expression declined drastically. We confirmed this trend in our multi-centric cohort of ASCT patients by comparing levels of DAT and ICA sampled at admission to the transplantation ward (Conditioning) versus at clinical diagnosis of GVHD: in patients with GVHD, metabolite levels were drastically reduced. Metabolite stimulation of mouse small intestinal organoids promoted organoid growth and required intact STING signaling. Additionally, organoids showed an increased stemness and resistance to T cell mediated damage. Both healthy donor and GvHD patient derived human colon organoids also responded to DAT and ICA, however the metabolite effect was lost when co-administered with the STING-inhibitor H151. Next, we prophylactically administered metabolites in a major mismatch mouse ASCT model. Metabolite-treated mice showed significantly better outcomes in barrier integrity and organoid based intestinal regeneration assays. Additionally, metabolite treatment was associated with an increased regulatory T cell infiltration. These effects were abrogated in STING-/- recipients, but not in IFNaR-/- recipients. Finally, metabolite treatment was protective in major mismatch GVHD mouse models. Conclusions: We identify that microbial-derived metabolites detected in patients can engage the STING pathway in humans and mice to confer resistance from immune damage. Thus, prophylactic administration of metabolite cocktails or bacterial consortia may reduce occurrence of GVHD in ASCT patients.

Exploring the Impacts of Full-Scale Distribution System Orthophosphate Corrosion Control Implementation on the Microbial Ecology of Hydrologically Connected Urban Streams.

Many cities across the nation are plagued by lead contamination in drinking water. As such, many drinking water utilities have undertaken lead service line (LSL) replacement to prevent further lead contamination. However, given the urgency of lead mitigation, and the socioeconomic challenges associated with LSL replacement, cities have used phosphate-based corrosion inhibitors (i.e., orthophosphate) alongside LSL replacement. While necessary to ensure public health protection from lead contamination, the addition of orthophosphate into an aging and leaking drinking water system may increase the concentration of phosphate leaching into urban streams characterized by century-old failing water infrastructure. Such increases in phosphate availability may cascade into nutrient and microbial community composition shifts. The purpose of this study was to determine how this occurs and to understand whether full-scale distribution system orthophosphate addition impacts the microbial ecology of urban streams. Through monthly collection of water samples from five urban streams before and after orthophosphate addition, significant changes in microbial community composition (16S rRNA amplicon sequencing) and in the relative abundance of typical freshwater taxa were observed. In addition, key microbial phosphorus and nitrogen metabolism genes (e.g., two component regulatory systems) were predicted to change via BugBase. No significant differences in the absolute abundances of total bacteria, Cyanobacteria, and "Candidatus Accumulibacter" were observed. Overall, the findings from this study provide further evidence that urban streams are compromised by unintentional hydrologic connections with drinking water infrastructure. Moreover, our results suggest that infiltration of phosphate-based corrosion inhibitors can impact urban streams and have important, as-yet-overlooked impacts on urban stream microbial communities. IMPORTANCE Elevated lead levels in drinking water supplies are a public health risk. As such, it is imperative for cities to urgently address lead contamination from aging drinking water supplies by way of lead service line replacements and corrosion control methods. However, when applying corrosion control methods, it is also important to consider the chemical and microbiological effects that can occur in natural settings, given that our water infrastructure is aging and more prone to leaks and breaks. Here, we examine the impacts on the microbial ecology of five urban stream systems before and after full-scale distribution system orthophosphate addition. Overall, the results suggest that infiltration of corrosion inhibitors may impact microbial communities; however, future work should be done to ascertain the true impact to protect both public and environmental health.

Compositional stability of sediment microbial communities during a seagrass meadow decline

The presence of seagrass shapes surface sediments and forms a specific environment for diverse and abundant microbial communities. A severe decline of Cymodocea nodosa, a widespread seagrass species in the Mediterranean Sea, has been documented. To characterise and assess the changes in microbial community composition during the decline of a Cymodocea nodosa meadow, Illumina MiSeq sequencing of the V4 region of the 16S rRNA gene was performed. Samples of surface sediments from two sites, one without any vegetation and one with a declining Cymodocea nodosa meadow, were collected at monthly intervals from July 2017 to October 2018. Microbial communities were stratified by sediment depth and differed between the vegetated and the nonvegetated site. Although the Cymodocea nodosa meadow declined to a point where almost no leaves were present, no clear temporal succession in the community was observed. Taxonomic analysis revealed a dominance of bacterial over archaeal sequences, with most archaeal reads classified as Nanoarchaeota, Thermoplasmatota, Crenarchaeota, and Asgardarchaeota. The bacterial community was mainly composed of Desulfobacterota, Gammaproteobacteria, Bacteroidota, Chloroflexi, Planctomycetota, and Campylobacterota. Our results show that sediment microbial communities are remarkably stable and may resist major disturbances such as seagrass meadow decline.

Changes in microbial community composition drive the response of ecosystem multifunctionality to elevated ozone

Increasing tropospheric ozone poses a potential threat to both above- and belowground components of the terrestrial biosphere. Microorganisms are the main drivers of soil ecological processes, however, the link between soil microbial communities and ecological functions under elevated ozone remains poorly understood. In this study, we assessed the responses of three crop seedlings (i.e., soybean, maize, and wheat) growth and soil microbial communities to elevated ozone (40 ppb O3 above ambient air) in a pot experiment in the solardomes. Results showed that elevated ozone adversely affected ecosystem multifunctionality by reducing crop biomass, inhibiting soil extracellular enzyme activities, and altering nutrient availability. Elevated ozone increased bacterial and fungal co-occurrence network complexity, negatively correlated with ecosystem multifunctionality. Changes in the relative abundance of some specific bacteria and fungi were associated with multiple ecosystem functioning. In addition, elevated ozone significantly affected fungal community composition but not bacterial community composition and microbial alpha-diversity. Crop type played a key role in determining bacterial alpha-diversity and microbial community composition. In conclusion, our findings suggest that short-term elevated ozone could lead to a decrease in ecosystem multifunctionality associated with changes in the complexity of microbial networks in soils.

Changes in the composition of bacterial communities and pathogen levels during wastewater treatment.

Wastewater treatment plants have been described as a potential source of spreading pathogens to the receiving water. However, few studies are reporting the presence and concentration changes of pathogens in these matrices. High-throughput sequencing provides new insights into understanding the changes of bacterial communities throughout wastewater treatment plants (WWTPs). In this study, the changes in microbial community composition and the levels of representative pathogens of effluents during the wastewater treatment process in two municipal WWTPs (A and B) were analyzed using Illumina NovaSeq sequencing and qPCR. Proteobacteria was the most abundant phylum in all samples, accounting for 45.0-75.2% of the bacterial community, followed by Firmicutes, Bacteroidetes, Actinobacteria, and Nitrospirae. A slight difference was observed between the bacterial community compositions of WWTPs A and B. However, a significant difference in the community compositions of effluent samples at different treatment stages was observed. Nutrients had a more substantial impact on bacterial community composition than physicochemical factors. Most human-associated Bacteroides and Mycobacterium were eliminated during the wastewater treatment process in both WWTPs. The bacterial community richness in WWTP A was significantly higher than that in WWTP B. The results of this study will provide insights into the potential problems that exist in WWTPs. In turn, these insights can enable the efficient and stable operation of WWTPs and help prevent the spread of pathogens.

Impact of Moso Bamboo (Phyllostachys edulis) Expansion into Japanese Cedar Plantations on Soil Fungal and Bacterial Community Compositions

Moso bamboo expansion is common across the world. The expansion of moso bamboo into adjacent forests altered plant and soil characteristics. While the community structure of soil fungi and bacteria plays an important role in maintaining the function of forest ecosystems, changes in microbial community compositions remain unclear, limiting our understanding of ecological process changes following moso bamboo expansion. To explore changes in the community structure of soil fungi and bacteria in Japanese cedar plantations experiencing expansion of moso bamboo, Illumina NovaSeq high-throughput sequencing technology was used to elucidate changes in soil microbial communities as well as alteration in litter and soil chemical characteristics. The results showed that moso bamboo expansion decreased content of soil organic carbon, total nitrogen, litter carbon, and the carbon to nitrogen ratio as well as the number of bacterial operational taxonomic units (OTUs) at the genus level, the α-diversity Simple index, and the abundance of Acidobacteria, Chloroflexi, and Gemmatimonadetes. Moso bamboo expansion also increased soil NH4+-N, pH, while it decreased fungi OTUs at the phyla, class, order, family, and genus level. The expansion of moso bamboo into Japanese cedar substantially altered soil fungal and bacterial community structure, which might have implications for changes in the ecosystem element-cycling process. In the forest ecosystem and expansion management of moso bamboo, the types and different expansion stages of moso bamboo should be paid attention to, in the assessment of ecological effects and soil microbial structure.

Low abundance members of the gut microbiome exhibit high immunogenicity

ABSTRACT Studies identifying bacterial members that dictate host phenotype have focused mainly on the dominant members, and the role of low abundance microbes in determining host phenotypes and pathogenesis of diseases remains unexplored. In this study, we compared the gut bacterial community of mice with wide-ranging microbial exposure to determine if low abundance bacteria vary based on microbial exposure or remain consistent. We noted that similar to the high abundance bacterial community, a core community of low abundance bacteria made up a significant portion of the gut microbiome irrespective of microbial exposure. To determine the role of low abundance bacteria in regulating community composition and host gene expression, we devised a microbiome dilution strategy to “delete” out low abundance bacteria and engrafted the diluted microbiomes into germ-free mice. Our approach successfully excluded low abundance bacteria from small and large intestinal bacterial communities and induced global changes in microbial community composition in the large intestine. Gene expression analysis of intestinal tissue revealed that loss of low abundance bacteria resulted in a drastic reduction in expression of multiple genes involved MHCII antigen presentation pathway and T-cell cytokine production in the small intestine. The effect of low abundance bacteria on MHCII expression was found to be specific to the intestinal epithelium at an early timepoint post-colonization and correlated with bacteria belonging to the family Erysipelotrichaceae. We conclude that low abundance bacteria have a significantly higher immuno-stimulatory effect compared to dominant bacteria and are thus potent drivers of early immune education in the gut.

Fungal Community Composition as Affected by Litter Chemistry and Weather during Four Years of Litter Decomposition in Rainshadow Coastal Douglas-Fir Forests.

Climate and litter chemistry are major factors influencing litter decay, a process mediated by microbes, such as fungi, nitrogen-fixing bacteria and ammonia-oxidizing bacteria. Increasing atmospheric CO2 concentrations can decrease nitrogen (N) and increase condensed tannin (CT) content in foliar litter, reducing litter quality and slowing decomposition. We hypothesized that reduced litter quality inhibits microbes and is the mechanism causing decomposition to slow. Litterbags of Douglas-fir needles and poplar leaves with a range of N (0.61–1.57%) and CT (2.1–29.1%) treatment and natural acid unhydrolyzable residue (35.3–41.5%) concentrations were placed along climatic gradients in mature Douglas-fir stands of coastal British Columbia rainshadow forests. The structure (diversity, richness and evenness) and composition of microbial communities were analyzed using DGGE profiles of 18S, NifH-universal and AmoA PCR amplicons in foliar litter after 7, 12, 24 and 43 months of decay. High CT and low N concentrations in leaf litter were associated with changes in microbial community composition, especially fungi. Contrary to our hypothesis, high CT and low N treatments did not inhibit microbial colonization or diversity. The joint effects of air temperature and soil moisture on microbial community composition at our sites were more important than the effects of initial litter chemistry.

Changes in microbial community composition affect bioactivities of mucus isolated from coral acropora millepora

Antibiotic resistance is increasingly popular together with emerging diseases presents an urgent requirement for more and more discovery of novel marine bioactive compounds. Paired-end reads of 16S rRNA sequence of bacteria living in the coral Acropora millepora obtained by the Illumina next-generation sequencing technology to be processed by DADA2 pipeline, phyloseq and ggplot2 packages showed that bleached coral mucus had an alpha diversity to be higher than healthy coral mucus. The coral surface mucus layer (SML) of healthy coral exhibited higher growth inhibition activity to Vibrio parahaemolyticus test strain than that of bleached coral in any amount (10 – 30 µL). The cytotoxicity against the colon cancer cell line HCT 116 was also clearly observed when treated with healthy SML and was 1.5 times higher than mucus was taken from bleached coral. The composition of the microbial community was shifted when corals changed from a healthy state to a bleached one, resulting in the reduction of antibacterial activity and cytotoxicity.

A 16S rRNA Sequencing Study Describing the Environmental Microbiota of Two Powdered Infant Formula Built Facilities.

Microbial safety is critically important for powdered infant formula (PIF) fed to neonates, with under-developed immune systems. The quality and safety of food products are dictated by those microorganisms found in both raw materials and the built production environment. In this study, a 2-year monitoring program of a production environment was carried out in two PIF factories located in the Republic of Ireland, and the environmental microbiome in different care areas of these sites was studied by using a 16S ribosomal RNA (rRNA)-based sequencing technique. Results highlighted a core microbiome associated with the PIF factory environment containing 24 bacterial genera representing five phyla, with Acinetobacter and Pseudomonas as the predominant genera. In different care areas of the PIF factory, as hygiene standards increased, deciphered changes in microbial community compositions became smaller over time and approached stability, and bacteria dominating the care area became less influenced by the external environment and more by human interactions and raw materials. These observations indicated that the microbial composition can be altered in response to environmental interventions. Genera Cronobacter and Salmonella were observed in trace amounts in the PIF factory environment, and bacterial genera known to be persistent in a stressed environment, such as Acinetobacter, Bacillus, Streptococcus, and Clostridium, were likely to have higher abundances in dry environment-based care areas. To our knowledge, this is the first study to characterize the PIF production environment microbiome using 16S rRNA-based sequencing. This study described the composition and changing trends of the environmental microbial communities in different care areas of the PIF manufacturing facility, and it provided valuable information to support the safer production of PIF in the future.

Responses of edaphic factors and microbial community to terrestrial succession and experimental warming in coastal salt marshes

To date, how the combined effects of terrestrial succession and climate warming will affect the edaphic factors and microbial community of coastal salt marshes remains unclear. To address this question, we compared the growth traits (i.e., morphology and biomass), edaphic properties, microbial community and function of Phragmites australis and Imperata cylindrica communities under natural vegetation succession (i.e., shift from P. australis to I. cylindrica) with or without warming treatment of I. cylindrica over two growing seasons (2019–2020). The results showed that after terrestrial succession, soil water content (SWC), electrical conductivity, clay content, total organic carbon and total nitrogen decreased significantly, while soil pH and contents of nitrate (NO3--N) and ammonium (NH4+-N) increased. The microbial community structure was greatly altered by terrestrial succession. The combination of terrestrial succession and experimental warming reinforced the change trends of SWC and pH but caused NO3--N and NH4+-N to decline to levels as low as those before succession. Although little response in microbial community structure was detected, the relative abundances of some dominant microorganisms and functional groups involved in C and N cycling were altered under the combination treatment. These variations in dominant microorganisms and predicted functional groups were related to changes in SWC, pH and particle size fractions and further influenced soil aeration and C/N availability. We concluded that in coastal salt marshes, experimental warming could further alter soil edaphic factors after terrestrial succession with little effect on microbial community structure. The changes in microbial community composition and function had a close correlation with edaphic factors. Our results suggested that adaptive soil management practices (i.e., inoculation of important microorganisms) should be considered to mitigate the soil degradation of coastal salt marshes with terrestrial succession under predicted climate warming.

Transfer of Nitrogen and Phosphorus From Cattle Manure to Soil and Oats Under Simulative Cattle Manure Deposition.

Simulated cattle manure deposition was used to estimate nutrient transfer to soil and oats and to investigate changes in microbial community composition and functional groups in oat rhizospheres. Nutrient absorption and return efficiency were calculated as a series of standard calculation formulas, and total nutrient transfer efficiency was nutrient absorption efficiency plus nutrient return efficiency. In total, 74.83% of nitrogen (N) and 59.30% of phosphorus (P) in cattle manure were transferred to soil and oats, with 11.79% of N and 7.89% of P in cattle manure absorbed by oats, and the remainder sequestered in the soil for 80 days after sowing. Cattle manure increased oat root length, surface, and volume under 0.2 mm diameter, and improved relative abundance of the microbiome known to be beneficial. In response to cattle manure, several bacteria known to be beneficial, such as Proteobacteria, Bacteroidota, and Firmicutes at phyla the level and Pseudoxanthomonas, Pseudomonas, and Sphingomonas at the genus level, were positively related to oat biomass and nutrient accumulation. For fungal communities, the relative abundance of Ascomycota is the predominant phylum, which varied in a larger range in the control treatment (81.0–63.3%) than the cattle manure deposition treatment (37.0–42.9%) as plant growing days extend. The relevant abundance of Basidiomycota known as decomposer was higher in cattle manure deposition treatment compared to that in control treatment at 15 days after sowing. More importantly, cattle manure deposition inhibited trophic mode within pathotroph like Alternaria and Fusarium fungal genus and promoted saprotroph and symbiotroph.