Higher Relative Abundance Research Articles

Biological Interactions and Environmental Influences Shift Microeukaryotes in Permafrost Active Layer Soil Across the Qinghai-Tibet Plateau.

Permafrost active layer soils are harsh environments with thaw/freeze cycles and sub-zero temperatures, harboring diverse microorganisms. However, the distribution patterns, assembly mechanism, and driving forces of soil microeukaryotes in permafrost remain largely unknown. In this study, we investigated microeukaryotes in permafrost active layer across the Qinghai-Tibet Plateau (QTP) using 18S rRNA gene sequencing. The results showed that the microbial eukaryotic communities were dominated by Nematozoa, Ciliophora, Ascomycota, Cercozoa, Arthropoda, and Basidiomycota in terms of relative abundance and operational taxonomic unit (OTU) richness. Nematozoa had the highest relative abundance, while Ciliophora had the highest OTU richness. These phyla had strong interactions between each other. Their alpha diversity and community structure were differently influenced by the factors associated to location, climate, and soil properties, particularly the soil properties. Significant but weak distance-decay relationships with different slopes were established for the communities of these dominant phyla, except for Basidiomycota. According to the null model, community assemblies of Nematozoa and Cercozoa were dominated by heterogeneous selection, Ciliophora and Ascomycota were dominated by dispersal limitation, while Arthropoda and Basidiomycota were highly dominated by non-dominant processes. The assembly mechanisms can be jointly explained by biotic interactions, organism treats, and environmental influences. Modules in the co-occurrence network of the microeukaryotes were composed by members from different taxonomic groups. These modules also had interactions and responded to different environmental factors, within which, soil properties had strong influences on these modules. The results suggested the importance of biological interactions and soil properties in structuring microbial eukaryotic communities in permafrost active layer soil across the QTP.

Microbiome dynamics during anaerobic digestion of food waste and the genetic potential for poly (lactic acid) co-digestion

Anaerobic digestion of food waste (FW) and potential co-digestion with biodegradable packaging material (i.e., bioplastics) have been promising resource recovery strategies. Unveiling the microbiome dynamics involved in the digestion process and exploring the genetic potential for poly (lactic acid) hydrolysis therein provide the fundamental basis for further process control and optimization. The current study has shown that the FW-digesting microbiome changed in both composition and activity-dormancy status while consuming available substrates. The microbiome assembly was mainly driven by homogeneous selection (36.7% on average) and drift (59.5% on average), and the homogeneous selection effect scaled with the availability of substrates. Based on the ratio between the relative activity and abundance, the microbiome was clustered into four groups. The Group 1 microbes, including Bacterioidetes_vadinHA17 and Syntrophomonadaceae, accumulated high relative abundance during the early stage of the digestion process but entered dormancy after the preferred substrate was consumed. Other members, i.e., the Group 4 Syntrophobacteraceae and Pseudomonadaceae, showed low abundance but disproportional activity during the later stage of the digestion process. The genome-centric metagenomics revealed that inherent AD microbes, especially the Group 1 microbes, harbored robust hydrolase genes, facilitating the PLA degradation. In fact, PLA addition to FW digestor led to significant methane production enhancement (14%) but negligible changes in microbiome composition. The outcome of this study provided the theoretical basis for developing microbiome management and engineering strategies that prospect efficient FW and PLA co-digestion processes.

Comparing Sediment Microbial Communities of Arctic Beaver Ponds to Tundra Lakes and Streams

AbstractIn recent decades the habitat of North American beaver (Castor canadensis) has expanded from boreal forests into Arctic tundra ecosystems. Beaver ponds in Arctic watersheds are known to alter stream biogeochemistry, which is likely coupled with changes in the activity and composition of microbial communities inhabiting beaver pond sediments. We investigated bacterial, archaeal, and fungal communities in beaver pond sediments along tundra streams in northwestern Alaska (AK), USA and compared them to those of tundra lakes and streams in north‐central Alaska that are unimpacted by beavers. β‐glucosidase activity assays indicated higher cellulose degradation potential in beaver ponds than in unimpacted streams and lakes within a watershed absent of beavers. Beta diversity analyses showed that dominant lineages of bacteria and archaea in beaver ponds differed from those in tundra lakes and streams, but dominant fungal lineages did not differ between these sample types. Beaver pond sediments displayed lower relative abundances of Crenarchaeota and Euryarchaeota archaea and of bacteria from typically anaerobic taxonomic groups, suggesting differences in rates of fermentative organic matter (OM) breakdown, syntrophy, and methane generation. Beaver ponds also displayed low relative abundances of Chytridiomycota (putative non‐symbiotic) fungi and high relative abundances of ectomycorrhizal (plant symbionts) Basidiomycota fungi, suggesting differences in the occurrence of plant and fungi mutualistic interactions. Beaver ponds also featured microbes with taxonomic identities typically associated with the cycling of nitrogen and sulfur compounds in higher relative abundances than tundra lakes and streams. These findings help clarify the microbiological implications of beavers expanding into high latitude regions.

Spatial distribution of antibiotic resistance genes in marine sediments of east China seas

ARGs were considered an emerging contaminant due to their ability to fail antibiotic therapy and extensive occurrence in various environmental matrices. A full profile of the occurrence of ARGs in seas is therefore critical for evaluating strategies to regulate ARGs pollution. This study performed a large-scale sampling in the seas of China and evaluated the abundance of ARGs. β-lactam resistance genes blaTEM were shown to be ubiquitous and predominant in all sea areas with the highest relative abundances up to 2.7 × 10−3, while clinically relevant vancomycin resistance genes (vanA) were only detected in the Bohai sea and held the lowest abundances of 5.2 × 10−7. The total ARG abundances in the sediments increased from north to south, where the South China Sea held the highest and the Bohai Sea held the lowest. Contents of nitrate, organic carbon and total carbon were major physicochemical properties that regulated the distribution and variation of blaTEM and tetC in the sediments. Bacteroidetes and Firmicutes were dominant potential host bacteria of blaTEM, tetC, sul1, and intI1. This study provides new insight into the pollution status of ARGs in sea areas of China, which contributes to ARGs risk assessment and raises awareness of managing antibiotic resistance pollution.

Application of an Integrated Granular and Suspended Sludge Methane Reactor for a Two-Stage Anaerobic Digestion System to Deal with Biodegradable Municipal Solid Waste

This study aims to investigate the performance of a two-stage anaerobic digestion system using a hybrid methane reactor to deal with biodegradable municipal solid waste. The reactor allowed both suspended sludge and granular sludge to work together. The feedstock was fermented in one continuous stirred tank at different pH conditions for 5 d. Furthermore, the liquid hydrolysate was diluted and pumped into a methane reactor with different organic loading rates. In the fermentative reactor, raising the pH condition from 4.5 to 6.5 caused a sharp increase in volatile fatty acids concentration, mainly due to the increase in acetate and propionate. The efficiency of the methane reactor was proven by the results of hydrodynamic analysis and biogas production. The relationship between biogas production and operating parameters in this reactor was modeled using a quadratic multivariate regression model. Overall, by maintaining the fermentative reactor at a pH of 6.0–6.5, the methane reactor was able to achieve an organic loading rate of 7.6 g-TS.L−1·d−1 with outstanding biogas quality and yield. In terms of microbiology, the most dominant phyla in the reactor included Firmicutes, Bacteroidetes, Proteobacteria, Euryarchaeota, Synergistetes, and Chloroflexi. Among them, the species with the highest relative abundance in granular sludge was Firmicutes, while that in suspended sludge was Bacteroidetes.

Oral and gut microbial biomarkers of susceptibility to respiratory tract infection in adults: A feasibility study

We conducted a feasibility cohort study which aimed to recruit and retain adults from the community to collect saliva (oral) and stool (gut) samples at three time points, at the start of the study (baseline), during a respiratory tract infection (RTI) and post-RTI. Community RTIs place a huge burden on health care services, and a non-invasive microbial diagnostic tool to predict the most vulnerable to respiratory infection would be ideal. To this aim, we analysed oral-gut baseline samples comparing those who reported RTI symptoms to those who remained healthy throughout the study for microbial biomarkers of respiratory susceptibility. Amplicon sequence variants (ASV) were identified by 16S sequence profiling to reveal oral-gut microbes. Reverse transcriptase-polymerase chain reaction (RT-PCR) was applied to target common respiratory microbes. Two general practices were recruited, and the participant recruitment rate was 1.3%. A total of 40 adult participants were retained, of which 19 acquired an RTI whereas 21 remained healthy. In healthy baseline oral and gut samples, ASVs from participants with RTI symptoms compared to those who remained healthy were similar with a high relative abundance of Streptococcus sp., and Blautia sp., respectively. Linear discriminant analysis effect size (LEfSe) revealed baseline oral microbes differed, indicating participants who suffered RTI symptoms had enhanced Streptococcus sobrinus and Megamonas sp., and depletion of Lactobacillus salivarius, Synergistetes, Verrucomicrobia and Dethiosulfovibrio. Furthermore, a random forest model ranked Streptococcus (4.13) as the highest mean decrease in accuracy (MDA) and RT-PCR showed a higher level of carriage of coagulase-negative Staphylococcus. Baseline core gut microbes were similar in both participant groups whereas LEfSe analysis revealed enhanced Veillonella, Rikenellaceae, Enhydobacteria, Eggerthella and Xanthomonsdales and depleted Desulfobulbus and Coprobacillus. Sutterella (4.73) had a high MDA value. Overall, we demonstrated the feasibility of recruiting and retaining adult participants from the community to provide multiple biological samples for microbial profiling. Our analyses identified potential oral-gut microbial biomarkers of respiratory infection susceptibility in otherwise healthy participants.

Control of particulate manganese (Mn) cycling in halocline Arctic Ocean waters by putative Mn‐oxidizing bacterial dynamics

AbstractParticulate Mn, given its high adsorptive capacity and oxidation potential, has profound impacts on the cycling of various trace elements and organic matter in the ocean. Moreover, particulate Mn acts as a sink (via oxidation and adsorption) or as a source (via remineralization and photoreduction) term of bioactive dissolved Mn(II). In the Canadian Arctic Ocean, particulate Mn distributions in the water column revealed the presence of distinctively high particulate Mn concentrations and an overwhelming dominance of the non‐lithogenic component to the bulk particulate Mn pool. This phenomenon is of particular importance in halocline waters in the Canada Basin, the Canadian Arctic Archipelago and Baffin Bay, and near‐bottom samples in Baffin Bay. Enhanced microbially‐mediated Mn oxidation in the water column is suggested as the main mechanism driving the non‐lithogenic dominance. Indeed, the microbial community composition data associated with high non‐lithogenic particulate Mn (i.e., Mn oxides) display a high relative abundance of taxa (e.g., f.Pirellulaceae, o.Phycisphaerales, f.Cryomorphaceae, g. Moritella) that have been identified in Mn oxide enriched environments. Furthermore, numerous taxa identified in the Canada Basin halocline water, where non‐lithogenic particulate Mn peaked, are phylogenetically related to known (cultured) Mn‐oxidizing bacteria (MnOB; e.g., Rhodobacteraceae, Oceanospirillaceae, Rhizobiaceae, and other Alphaproteobacteria). Putative MnOB appears to proliferate in certain water masses having a unique set of environmental conditions: low light intensity—alleviating photoinhibition—and high dissolved Mn concentrations, the main drivers known to influence MnOB dynamic, and hence, Mn oxidation.

Small-mammal abundance and species diversity: land use and seasonal influences in the Serengeti Ecosystem, Tanzania

Land use, habitat suitability, and seasonality can fundamentally shape small-mammal abundance, species richness, diversity, evenness, and composition. However, how these characteristics of small mammals are determined by land use, habitat type, and rainfall seasonality is still poorly understood for most ecosystems. We analyze how land use (protection in a national park, pastoralism, and crop agriculture), habitat type, and rainfall seasonality influence small-mammal relative abundance, species richness, and diversity in the Tanzania Serengeti Ecosystem. We used 141 live traps to capture 612 small mammals in the wet and dry seasons of 2017 and 2018. Relative abundance was higher in the pastoral land than in the park or agricultural land and in the dry season in all the three land use types. Species richness and diversity were highest in the park, middling in the agricultural land, and lowest in the pastoral land. The high relative abundance in the pastoral land was primarily due to the numerical dominance of two generalist species in the shrubland (grass rat Arvicanthis niloticus) and cropland (multimammate rat Mastomys natalensis), resulting in low species richness and diversity. High species richness and diversity in the park indicate high habitat heterogeneity, whereas high species diversity in the agricultural land during the dry season reflects high food availability during and soon after harvests. Thus, human activities apparently exert deleterious effects on some specialist small mammals as a result of reduced habitat heterogeneity while promoting the abundance of some generalist species in African savanna ecosystems. However, increased abundance of generalist species reduces small mammal species diversity while increasing the risk of human–small mammal conflicts. We offer several testable hypotheses motivated by our results.

Zinc accumulation in Atriplex lentiformis is driven by plant genes and the soil microbiome

Successful phytoremediation of acidic metal-contaminated mine tailings requires amendments to condition tailings properties prior to plant establishment. This conditioning process is complex and includes multiple changes in tailings bio-physico-chemical properties. The objective of this project is to identify relationships between tailings properties, the soil microbiome, and plant stress response genes during growth of Atriplex lentiformis in compost-amended (10 %, 15 %, 20 % w/w) mine tailings. Analyses include RNA-Seq for plant root gene expression, 16S rRNA amplicon sequencing for bacterial/archaeal communities, metal concentrations in both tailings and plant organs, and phenotypic measures of plant stress. Zn accumulation in A. lentiformis leaves varied with compost levels and was the highest in the intermediate treatment (15 %, TC15). Microbial analysis identified Alicyclobacillus, Hydrotalea, and Pseudolabrys taxa with the highest relative abundance in TC15, and these taxa were strongly associated with Zn accumulation. Furthermore, we identified 190 root genes with significant gene expression changes. These root genes were associated with different pathways including, abscisic acid and auxin signaling, defense responses, ion channels, metal ion binding, oxidative stress, transcription regulation, and transmembrane transport. However, root gene expression changes were not driven by the increasing levels of compost. For example, there were 15 genes that were up-regulated in TC15, whereas 106 genes were down-regulated in TC15. The variables analyzed explained 86 % of the variance in Zn accumulation in A. lentiformis leaves. Importantly, Zn accumulation was driven by Zn shoot concentrations, leaf stress symptoms, plant root genes, and microbial taxa. Therefore, our results suggest there are strong plant-microbiome associations that drive Zn accumulation in A. lentiformis and different plant gene pathways are involved in alleviating varying levels of metal stress. Future work is needed to gain a mechanistic understanding of these plant-microbiome interactions to optimize phytoremediation strategies as they will govern the success or failure of the revegetation process.

Population Dynamics of Dragonflies at The Paddy Field Ecosystem, Sidorejo, Central Bengkulu

The rice fields of Sidorejo Village have the potential for dragonfly diversity. This study aims to analyze fluctuations in the diversity and abundance of dragonflies in three ecosystem conditions of rice fields in Sidorejo Village, Bengkulu Tengah. Sampling using purposive sampling with the cruising method. Data analysis was carried out descriptively through the identification of characteristics to obtain the name of the species. After the species name was obtained, the relative abundance, Shannon Wienner diversity index, and species evenness index were calculated. The results of the study found that the harvest ecosystem had the highest diversity and abundance of dragonflies (13 species and 45 individuals). The species that were consistently found in three types of ecosystems were Orthetrum sabina, O. testaceum, and Pantala flavescens. The species with the highest relative abundance was O. sabina with 32%. The diversity index ranged from 1.32 (post-harvest) to 2.25 (harvest). The highest evenness index was in the post-harvest ecosystem at 0.95, and the lowest was in the harvest ecosystem at 0.87. The results of this study are expected to show that the diversity and abundance of dragonflies fluctuate depending on seasonal ecosystem conditions in the rice fields.

Effects of Transplantation and Microhabitat on Rhizosphere Microbial Communities during the Growth of American Ginseng

Transplanting has been widely used in American ginseng (Panax quinquefolium L.) cultivation in Northwest China to mitigate the negative effects of continuous cropping obstacles. Because of the accumulation of pathogenic microorganisms and the change in soil properties, transplanting American ginseng to newly cultivated fields after two years of growth has become a major planting pattern. Despite transplanting improving the quality of American ginseng, the effects of soil properties and microbiota on growth during the transplanting process are poorly understood. In the present study, microbial communities, soil physico-chemical properties and morpho-physiological parameters were analyzed to investigate the effects of microbiota and soil characteristics on American ginseng growth in both soil and ginseng root microhabitats. Results indicated that the structure and species of bacterial and fungal communities changed significantly in different microhabitats before and after transplantation. Moreover, the assemblage process of the bacterial community was dominated by deterministic processes. The stochastic process ratio increased and niche breadth decreased significantly after transplanting. While the assembly of the fungal community was dominated by stochastic process, and there was no significant difference in NST, βNTI or niche breadth before and after transplanting. Bacterial co-occurrence networks demonstrated a higher connectivity but a lower aggregation in soil microhabitat, while the fungal community networks remained stable before and after transplantation. Gammaproteobacteria was the biomarker in the soil microhabitat, while Alphaproteobacteria, Betaproteobacteria and Gemmatimonadetes were biomarkers in the ginseng root microhabitat. Sordariomycetes was a biomarker with high relative abundance in the fungal community before and after transplanting. The bacterial functional and important ASVs were significantly correlated with pH, organic matter, total nitrogen, available phosphorus, total potassium root fresh weight, taproot diameter and stem height of American ginseng. Partial least squares path modeling showed that soil properties significantly affected the formation of different microbial specific ASVs. The important functional ASVs in ginseng root microhabitat had a positive effect on American ginseng growth, while the rare taxa had a negative effect. Our results provide a good starting point for future studies of microbial community succession in different microhabitats influenced by the transplantation pattern of American ginseng.

Metaproteomic Analysis of Gut Resistome in the Cecal Microbiota of Fattening Pigs Raised without Antibiotics.

Improper use of antibiotics in swine could reduce commensal bacteria and possibly increase pathogen infections via the gut resistome. This study aimed to compare the metaproteomic profiles of the gut resistome and related metabolism in the cecal microbiota of fattening pigs raised under antibiotic-free (ABF) conditions with those of ordinary industrial pigs (controls [CTRL]). The top three relatively abundant microbes in both groups were Escherichia coli, Ruminococcus, and Lactobacillus, followed by Bacteroides and Bifidobacterium. E. coli, Lactobacillus, and Bacteroides were found to be increased in the CTRL group, whereas Ruminococcus and Clostridium were greater in the ABF group. The highest abundances of antibiotic resistance proteins (log2 expression levels [ELs] of >10) were found to be for tetracycline resistance (Tetr) and aminoglycoside resistance (AMGr) proteins found in Bacteroides, with a significant increase in the CTRL group. High Tetr (ELs of 5.32) was found in Ruminococcus in the CTRL group, although pigs in both groups had never received tetracycline, possibly reflecting the influence of environments in farms. In E. coli, AMGr and β-lactamase family proteins were observed in both groups (ELs of 3 to 6), whereas multidrug resistance protein MdtL was significantly expressed in the CTRL group (ELs of around 3). In the ABF group, CRISPR-associated endonucleases Cas1 and Cas9, which function to defend against viruses, were markedly observed in Ruminococcus and Lactobacillus, respectively, with ELs of 8.6 and 4.15, respectively. In conclusion, this study demonstrated that CRISPR-associated endonucleases were markedly observed in the ABF group, whereas higher levels of Tetr, AMGr, and multidrug resistance protein MdtL was markedly observed in dominant bacterial species in the CTRL group. IMPORTANCE In order to control and reduce antibiotic use in animals, the Department of Livestock Development, Thailand, has launched a campaign for antibiotic-free livestock production. The present study has shown for the first time that CRISPR-associated endonucleases Cas1 and Cas9, which function to defend against viruses, were markedly observed in Ruminococcus and Lactobacillus, respectively, in ceca of pigs raised without antibiotics (ABF). The highest abundances of antibiotic resistance proteins were for tetracycline (Tetr) and aminoglycoside resistance (AMGr) proteins found in Bacteroides, with a significant increase in the controls. In E. coli, the microbe with the highest relative abundance, AMGr and β-lactamase family proteins were observed in both groups, whereas multidrug resistance protein MdtL was significantly expressed in the controls. Pigs in both ABF and control groups had never received tetracycline, possibly reflecting the influence of farm environments. We suggest that pigs raised without antibiotics may have more beneficial microorganisms for the gut than pigs raised with antibiotics.

Home range, space use, and vertical distribution of Nassau grouper (Epinephelus striatus) during non-spawning times in Western Puerto Rico

Understanding animal space use patterns is critical for ecological research and conservation efforts. An organism’s home range territory serves as the fundamental unit of space use and is the area repeatedly used for routine activities. Nassau grouper, Epinephelus striatus, once of high commercial fishery importance, are now on the IUCN’s Red List designated as Critically Endangered due to overexploitation. Known for the formation of large spawning aggregations, information on their movements and space use dynamics outside of the reproductive period are lacking. In this study, we used acoustic telemetry to quantify the non-spawning horizontal and vertical space use patterns of Nassau grouper at the Bajo de Sico seamount, a seasonally closed marine protected area (MPA) in Puerto Rico. Twenty-nine groupers were tagged with acoustic transmitters, of which, fourteen were tracked continuously over a three-year period. Tagged individuals displayed high site fidelity to home reef locations and individuals occupied home ranges of relatively small size that remained constant between years. There was a high degree of overlap of home range territories and in locations where multiple individuals occupied the same home reef, individuals maintained discrete vertical distributions. Nassau groupers were recorded making multiple forays to the spawning site outside of the reported spawning season, and two individuals underwent home reef site relocation. Results indicate relatively low contribution to ecological connectivity during the non-reproductive period, therefore high relative abundances of this species are needed to fulfill their ecological role at the community level. The results also highlight the importance of Bajo de Sico, an isolated seamount of relatively deeper depth, as critical habitat for primary home reef sites of Nassau grouper. These results provide a basis for adapting the current management strategy at this MPA to provide adequate protection to the non-spawning population of Nassau grouper.

Biological Evaluation and Key Stress Factor Diagnosis of Compound Contaminated Soil Based on Environmental DNA

Healthy biological community composition and diversity are the basis for soil ecosystems to provide complete ecological functions and services. The current technical bottleneck in soil pollution control is the lack of systematic and comprehensive biodiversity indicators. In this study, the compound-polluted soil in an industrial park was taken as the object, and environmental DNA (eDNA)technology was used to monitor and analyze the composition of the biological community in the polluted soil. The environmental DNA-species sensitivity distribution (eDNA-SSD) method was constructed to diagnose the key stress factors and their ecological threshold. The results showed that:① compound pollution did not have a significant impact on the α-diversity of soil organisms in the park but led to changes in the composition of biological communities and dominant species with high relative abundance. The dominant groups in the polluted soil were Proteobacteria (25.54%), Ascomycota (15.65%), Actinobacteria (8.75%), and Chloroflexi (7.64%). ② Environmental factors accounted for 51.27% of the differences in soil biodistribution, and aniline, sulfate, petroleum hydrocarbon, and lead were the key stress factors for soil biomes. Among them, aniline had the most significant effect on the community distribution of bacteria (P=0.030), sulfate on fungi (P=0.025), and metazoans (P=0.032). ③ The ecological risk threshold (hazardous concentration for 5% of species, HC5) of pollutants with 95% species as the protection target showed a gradient decreasing trend of sulfate (470.00 mg·kg-1), petroleum hydrocarbon (17.00 mg·kg-1), lead (13.00 mg·kg-1), arsenic (6.20 mg·kg-1), 4-chloroaniline (0.16 mg·kg-1), and aniline (0.11 mg·kg-1). Nevertheless, the existing soil risk control value was significantly higher than the ecological risk value, indicating that the existing control standards targeting human health were not suitable for protecting soil health. The comprehensive pollution index showed that the soil pollution in the park was mostly mild pollution accompanied by heavy pollution at individual points. The biological evaluation method based on eDNA-SSD could achieve the comprehensive evaluation of composite pollution in the absence of the benchmark value of pollutants and at the same time better distinguish the differences in soil biological community structure and composition under different pollution levels (P=0.053). In conclusion, the environmental DNA soil biomonitoring and assessment method developed in this study has guiding significance and application value for soil ecosystem restoration assessment.

Effects of Cellulase and Xylanase Addition on Fermentation Quality, Aerobic Stability, and Bacteria Composition of Low Water-Soluble Carbohydrates Oat Silage

Most oat forage has low water-soluble carbohydrates (WSC), which may be the main limited factor for silage fermentation safely, but oat is rich in cellulose and hemicellulose; therefore, we assume that xylanase and cellulase as additives can reduce the content of cellulose and xylan in oat silage, increase the microbial fermentable sugar content, and improve the fermentation quality of the silage. After wilting, oats were treated as follows: (i) distributed water (CK); (ii) silages inoculated with xylanase (X); (iii) silages inoculated with cellulase (C), ensiling for 3 days (early stage of silage) and 60 days (late stage of silage), respectively, after ensiling 60 days for a 5-day aerobic exposure study. The pH, neutral detergent fiber (NDF), and acid detergent fiber (ADF) were significantly reduced by xylanase and cellulase treatment during the late stage of silage, and the concentration of lactic acid, acetic acid, and ammonia nitrogen increased remarkably. The WSC content reached its peak with xylanase treatment during the late stage of silage. The content of crude protein (CP) was not affected by additives but by the silage period; CP and ether extract (EE) significantly increased during the late stage of silage compared to the early stage. After ensiling, the bacterial community showed that xylanase and cellulase treatment increased the relative abundance of lactic acid bacteria. Lactobacillus has a higher relative abundance with cellulase treatment after 60 days of ensiling; this can effectively reduce the pH of silage and ensure long-term, stable storage of silage. Cellulase and xylanase increased bacterial diversity during aerobic exposure and improved the aerobic stability of silage significantly. This study indicated that different additives and silage periods had significant effects on chemical compositions, fermentation quality, and bacterial community; meanwhile, both additives improved the aerobic stability of silage. In summary, when the WSC of oat is low, cellulase and xylanase have good effects as silage additives, and the comprehensive effect of cellulase is more prominent.

A microbial consortium alters intestinal Pseudomonadota and antimicrobial resistance genes in individuals with recurrent Clostridioides difficile infection.

Intestinal colonization with pathogens and antimicrobial-resistant organisms (AROs) is associated with increased risk of infection. Fecal microbiota transplant (FMT) has successfully been used to cure recurrent Clostridioides difficile infection (rCDI) and to decolonize intestinal AROs. However, FMT has significant practical barriers to safe and broad implementation. Microbial consortia represent a novel strategy for ARO and pathogen decolonization, with practical and safety advantages over FMT. We undertook an investigator-initiated analysis of stool samples collected from previous interventional studies of a microbial consortium, microbial ecosystem therapeutic (MET-2), and FMT for rCDI before and after treatment. Our aim was to assess whether MET-2 was associated with decreased Pseudomonadota (Proteobacteria) and antimicrobial resistance gene (ARG) burden with similar effects to FMT. Participants were selected for inclusion if baseline stool had Pseudomonadota relative abundance ≥10%. Pre- and post-treatment Pseudomonadota relative abundance, total ARGs, and obligate anaerobe and butyrate-producer relative abundances were determined by shotgun metagenomic sequencing. MET-2 administration had similar effects to FMT on microbiome outcomes. The median Pseudomonadota relative abundance decreased by four logs after MET-2 treatment, a greater decrease than that observed after FMT. Total ARGs decreased, while beneficial obligate anaerobe and butyrate-producer relative abundances increased. The observed microbiome response remained stable over 4 months post-administration for all outcomes. IMPORTANCE Overgrowth of intestinal pathogens and AROs is associated with increased risk of infection. With the rise in antimicrobial resistance, new therapeutic strategies that decrease pathogen and ARO colonization in the gut are needed. We evaluated whether a microbial consortium had similar effects to FMT on Pseudomonadota abundances and ARGs as well as obligate anaerobes and beneficial butyrate producers in individuals with high Pseudomonadota relative abundance at baseline. This study provides support for a randomized, controlled clinical trial of microbial consortia (such as MET-2) for ARO decolonization and anaerobe repletion.

Metagenomic Insights Reveal the Microbial Diversity and Associated Algal-Polysaccharide-Degrading Enzymes on the Surface of Red Algae among Remote Regions

Macroalgae and macroalgae-associated bacteria together constitute the most efficient metabolic cycling system in the ocean. Their interactions, especially the responses of macroalgae-associated bacteria communities to algae in different geographical locations, are mostly unknown. In this study, metagenomics was used to analyze the microbial diversity and associated algal-polysaccharide-degrading enzymes on the surface of red algae among three remote regions. There were significant differences in the macroalgae-associated bacteria community composition and diversity among the different regions. At the phylum level, Proteobacteria, Bacteroidetes, and Actinobacteria had a significantly high relative abundance among the regions. From the perspective of species diversity, samples from China had the highest macroalgae-associated bacteria diversity, followed by those from Antarctica and Indonesia. In addition, in the functional prediction of the bacterial community, genes associated with amino acid metabolism, carbohydrate metabolism, energy metabolism, metabolism of cofactors and vitamins, and membrane transport had a high relative abundance. Canonical correspondence analysis and redundancy analysis of environmental factors showed that, without considering algae species and composition, pH and temperature were the main environmental factors affecting bacterial community structure. Furthermore, there were significant differences in algal-polysaccharide-degrading enzymes among the regions. Samples from China and Antarctica had high abundances of algal-polysaccharide-degrading enzymes, while those from Indonesia had extremely low abundances. The environmental differences between these three regions may impose a strong geographic differentiation regarding the biodiversity of algal microbiomes and their expressed enzyme genes. This work expands our knowledge of algal microbial ecology, and contributes to an in-depth study of their metabolic characteristics, ecological functions, and applications.

Microbial Communities Associated with Alternative Fuels in Model Seawater-Compensated Fuel Ballast Tanks

The biocorrosion of carbon steel poses a risk for ships combining seawater and fuel in metal ballast tanks. Ballast tanks were simulated by duplicate reactors containing carbon steel coupons and either petroleum F76 (petro-F76), Fischer–Tropsch F76 (FT-F76), or a 1:1 mix of both fuels, to investigate whether the alternative fuel FT-F76 influenced this risk. The polycarbonate reactors were inoculated with seawater, and the control reactors did not receive fuel. The reactors were monitored for 400 days, and they all reached a pH and open circuit potential where elemental iron was oxidized, indicating corrosion. The reactors containing petro-76 or fuel mix had higher levels of dissolved iron; one of each replicate had lower concentrations of sulfate than the original seawater, while the sulfate concentration did not decrease in the other incubations. The high sulfate reactors, but not the low sulfate reactors, had a high relative abundance of microaerophilic sulfide-oxidizing bacteria. The FT-F76 and the no-fuel reactors had a high relative abundance of iron-sequestering Magnetovibrio. Although dissolved iron and loss of sulfate under anoxic conditions are associated with biocorrosion, our results suggest that in our reactors these indicators were altered by iron-sequestering and sulfide-oxidizing microbes, which is consistent with the slow diffusion of oxygen across the polycarbonate reactors.

Batch-fed composting of food waste: Microbial diversity characterization and removal of antibiotic resistance genes

The aim of this work was to study the impact of batch-fed strategies on bacterial communities and ARGs in compost. The findings demonstrate that batch-feeding helped maintain high temperatures in the compost pile for an extended period (above 50 °C for 18 days), which in turn facilitated water dissipation. High-throughput sequencing showed that Firmicutes played a significant role in batch-fed composting (BFC). They had a high relative abundance at the beginning (98.64%) and end (45.71%) of compost. Additionally, BFC showed promising results in removing ARGs, with reductions of 3.04–1.09 log copies/g for Aminoglycoside and 2.26–2.44 log copies/g for β_Lactamase. This study provides a comprehensive survey of BFC and demonstrates its potential for eliminating resistance contamination in compost.

Mineral-solubilizing microbial inoculant positively affects the multifunctionality of anthropogenic soils in abandoned mining areas

The mining industry has a significant negative impact on ecosystems, and the remediation of abandoned mining sites requires effective strategies. One promising approach is the incorporation of mineral-solubilizing microorganisms into current external soil spray seeding technologies. These microorganisms possess the ability to decrease mineral particle sizes, promote plant growth, and enhance the release of vital soil nutrients. However, most previous studies on mineral-solubilizing microorganisms have been conducted in controlled greenhouse environments, and their practical application in field settings remains uncertain. To address this knowledge gap, we conducted a four-year field experiment at an abandoned mining site to investigate the efficacy of mineral-solubilizing microbial inoculants in restoring derelict mine ecosystems. We assessed soil nutrients, enzyme activities, functional genes, and soil multifunctionality. We also examined microbial compositions, co-occurrence networks, and community assembly processes. Our results demonstrated that the application of mineral-solubilizing microbial inoculants significantly enhanced soil multifunctionality. Interestingly, certain bacterial phyla or class taxa with low relative abundances were found to be key drivers of multifunctionality. Surprisingly, we observed no significant correlation between microbial alpha diversity and soil multifunctionality, but we did identify positive associations between the relative abundance and biodiversity of keystone ecological clusters (Module #1 and #2) and soil multifunctionality. Co-occurrence network analysis revealed that microbial inoculants reduced network complexity while increasing stability. Additionally, we found that stochastic processes played a predominant role in shaping bacterial and fungal communities, and the inoculants increased the stochastic ratio of microbial communities, particularly bacteria. Moreover, microbial inoculants significantly decreased the relative importance of dispersal limitations and increased the relative importance of drift. High relative abundances of certain bacterial and fungal phyla were identified as major drivers of the microbial community assembly process. In conclusion, our findings highlight the crucial role of mineral-solubilizing microorganisms in soil restoration at abandoned mining sites, shedding light on their significance in future research endeavors focused on optimizing the effectiveness of external soil spray seeding techniques.