Higher Relative Abundance Research Articles

Effects of water masses on the zooplankton community structure in the northern East China Sea during the East Asian Summer Monsoon in 2020

The prolonged rainy season in 2020 was classified as the second-largest rainfall event since 1961. In this study, we conducted a survey to assess fluctuations in the zooplankton community structure of the northern East China Sea (nECS) after the rainy season in August 2020. We examined 24 stations and observed several environmental factors, including water temperature, salinity, chlorophyll-a concentration, suspended particulate matter (SPM), and phytoplankton density. Zooplankton samples were collected from 12 stations using MOCNESS to target the surface mixed layer (SML), pycnocline layer (PNC), and lower layer (LL). In regions with low water temperatures, the Yellow Sea and northern East China Sea shelf mixed water community in each layer exhibited a decrease in the relative abundance of Calanus sinicus, whereas the incidence of Paracalanus parvus s. l. showed an increasing trend. Similarly, in areas with low salinity, the CDW and northern East China Sea shelf mixed water community in SML and PNC displayed comparable distributions, with a tendency for the relative abundance of Acartia pacifica and Paracalanus parvus s. l. to show a replacement pattern. Moreover, the Tsushima Warm Current (TWC) community in each layer, characterized by high water temperature and salinity, showed a high relative abundance of Oncaea spp. and a diverse species distribution, mainly in the eastern part of the study area. Our study identified multiple vertically distributed communities, providing detailed information on water mass structures through cluster analysis. This approach enhanced previous studies by offering novel insights into the vertical structure of water masses and their association with zooplankton communities in the nECS.

Quantitative assessment and seasonal incidence of soil invertebrates in okra (Abelmoschus esculentus L.) crop

The present study on population dynamics and diversity of soil invertebrates was carried out at Vegetable Research Farm, Punjab Agricultural University, Ludhiana during 2019. The study revealed that okra crop harboured 14 different soil invertebrate species belonging to nine orders and 13 families dominated by order coleoptera (five species) dominated by ground beetles. Interestingly, higher relative abundance (%) was recorded in order hymenoptera (80.72%) followed by polyzoniida (10.41%) among which higher dominance (%) was recorded in little black ants (80.78%). Species richness, species evenness, Shannon-Wiener index (H’) and Simpson’s index were calculated to be 14.0, 0.094, 0.098 and 0.051, respectively, indicating high degree of diversity among soil invertebrates in okra crop. Interestingly, an increase of 88.84 and 69.64% in population was recorded in root-knot and free-living/predatory nematodes at harvest time compared to the okra crop sowing time. A positive correlation (r=+0.06 to + 0.83) was recorded between soil temperature and soil moisture with soil invertebrate population. Okra crop fields survive soil fauna, which is a key factor for increasing soil fertility and productivity and its physical characteristics, which should be increased using soil amendments.

Association between endometrial microbiome and implantation success in women with frozen embryo transfer: results of a prospective cohort study

The aim of this prospective study was to compare the endometrial microbiome between pregnant and non-pregnant women after frozen embryo transfer (FET) with euploid embryos. Endometrial biopsies were collected from 30 women during the mid-luteal phase in a natural cycle. FET was performed with euploid embryos up to 3 months after the biopsy. Endometrial microbiota composition was analysed using 16S rRNA (v4-v5 region) next generation sequencing (NGS). The analysis of different clinical outcomes after the biopsy (no pregnancy (n = 14), and ultrasound confirmed pregnancy (n = 16)) revealed differences in the endometrial microbiome composition. In total, 271 distinct bacterial species and 668 bacterial genera were identified. The number of unique species found in non-pregnant women was 62 (22.88%), while in the patients who became pregnant after FET it was 39 (14.39%). Among them, bacteria with high frequency of occurrence such as Bacteroides spp., Cutibacterium granulosum, Isoptericola spp., Acetomicrobium spp., Marivivens spp. and Syntrophomonas spp. were found only in non-pregnant patients, while Bosea spp. was present only in pregnant women. The analysis of bacteria relative abundance revealed that Lactobacillus genus was not significantly different between the studied groups. In contrast, Serratia marcescens, Staphylococcus spp., Glutamicibacter spp. and Delftia spp. were significantly enriched in the non-pregnant group. In conclusion, specific bacteria taxa had higher relative abundance in the endometrium of patients with implantation failure after FET with euploid embryos. We hypothesize that an appropriate treatment for optimization of endometrial microbiome content in women with diagnosed microbiome dysbiosis could be beneficial for improvement of pregnancy rates.

Terrestrial versus aquatic source identification of sedimentary n-alkane and sugar biomarkers: a case study from the Bale Mountains, Ethiopia

Organic matter in sedimentary archives is abundantly used to reconstruct paleoenvironmental and climate histories. Thereby, distinguishing between the terrestrial and aquatic origin of sedimentary organic matter is often a prerequisite for robust interpretations. In this case study, we use published data for modern plants and topsoils to identify the terrestrial versus aquatic source of n-alkane and sugar biomarkers in two afro-alpine sediment archives (Lake Garba Guracha and Depression B4) in the Bale Mountains, Ethiopia. The results of our comparative approach show that the long-chain n-alkanes C29, C31, and C33 in the sedimentary archives yielded patterns similar to those typical for the potential terrestrial input. By contrast, the relative abundances of the sedimentary mid-chain n-alkanes C23 and C25, and at least partly C27, are significantly increased compared to the plants and topsoils. This suggests that they are primarily produced by aquatic macrophytes and micro-organisms. The Paq ratio (C23 + C25)/(C23 + C25 + C29 + C31) is validated as a suitable source identification proxy in our study area. The sugar biomarkers xylose (xyl) and arabinose (ara) are abundant in the plant and topsoil samples. By comparison, high relative abundances of fucose (fuc) and rhamnose (rham) are generally only observed in sediments. This indicates that these sugar biomarkers are primarily produced by aquatic macrophytes or micro-organisms. Therefore, the ratio (fuc + rham)/(ara + xyl) is a suitable sugar biomarker proxy for organic matter source identification. The relative abundances of galactose and mannose are systematically decreasing and increasing, respectively, from leaves over O-layers to Ah-horizons. Furthermore, they are not significantly different from the abundances found in the sediments. This hinders terrestrial versus aquatic source identification using galactose and mannose.

Effects of adding cocoa fermentation medium on cigar leaves in agricultural fermentation stage.

Background and Objective: With the development of the world economy and the integration of cultures, the Chinese cigar market has shown a significant upward trend. However, high-quality cigar leaves are mostly produced in Dominica, Cuba, Nicaragua and other places. In contrast, Chinese cigar leaves have problems such as insufficient aroma, which has become one of the main factors restricting the development of Chinese cigars. Adding medium to ferment is a traditional method in the cigar industry. At present, it mostly relies on manual experience, and lacks systematic and scientific research. At the same time, the addition of medium fermentation is mainly concentrated in the industrial fermentation process, and has not yet begun to be applied in the agricultural fermentation process. In this study, the medium was added to the agricultural fermentation process for the first time to explore the possibility of the application. The effects of adding cocoa medium to ferment on the chemical composition, sensory quality and surface microbial diversity of eggplant core cigar leaves were investigated.wrapper. Method: With Dexue 7' as the experimental material, the changes of main chemical components of wrapper fermented with water and cocoa medium were determined, and microbial community structure on the surface and relative abundance of cigar leaves at different turning periods were analyzed, and the functional genes were predicted. The results of the study were as follows: 1) The results of sensory evaluation showed that the addition of cocoa medium could highlight the aroma of bean, cocoa and coffee, improve the sweetness and fluency and the combustibility of cigar leaves. 2) The addition of cocoa medium increased the contents of proline and malic acid which were positively correlated with sensory quality, and decreased the contents of citric acid, linoleic acid, basic amino acids and aromatic amino acids which were negatively correlated with sensory quality. 3) The addition of cocoa medium increased the total amount of aroma components in cigar leaves, especially carotenoid degradation products, and changed the structural composition of some aroma substances in wrappercigar leaves. 4) The similarity of species composition between the water-added group and the cocoa-added group was higher, but the dominant microorganisms were more concentrated. Staphylococcus and Arthrobacter maintained a high relative abundance throughout the fermentation process, which may be the key microorganisms in the agricultural fermentation stage. 5) The addition of cocoa medium increased the expression abundance of related functional genes in cigar leaves, accelerated the fermentation process of cigar leaves, and bacteria played a major role in the fermentation process. Conclusion: Adding cocoa medium in the agricultural fermentation stage, the changes of bacterial community and dominant flora on the surface of cigar leaves are the main factors affecting their internal chemical components, and the addition of media has a positive effect on tobacco fermentation.

Characterization of rumen microbiota in lactating Holstein cows fed molasses versus corn grain at two levels of rumen-degradable protein

We evaluated the influence of diets differing in non-fiber carbohydrates and rumen-degradable protein (RDP) levels on changes in the ruminal bacterial populations in lactating Holstein cows. In all, 12 ruminally cannulated cows were assigned to diets with high or low RDP levels. Within each RDP level, molasses was substituted for corn grain at a concentration of 0%, 5.25%, or 10.5% of diet dry matter in a replicated 3 × 3 Latin square design with 28-day periods. Liquid and solid rumen digesta fractions collected at the end of each period underwent 16S rRNA gene sequencing to identify operational taxonomic units and were analyzed for short-chain fatty acids. Protein degradability affected 6 bacterial genera, whereas carbohydrate alteration impacted 13 genera (p < 0.05). Of the 30 genera with the highest relative abundance, 26 differed by digesta fraction (p < 0.05), with Bacteroidetes genera showing a greater abundance in solids and Firmicutes genera demonstrating a greater prevalence in liquids. Regarding relative abundances, with increasing molasses, Succiniclasticum decreased in liquid (p < 0.05), and CF231, YRC22, Clostridium, Desulfovibrio, BF311, and Oscillospira increased in solids (p < 0.05). In contrast, at higher RDP levels, Succiniclasticum increased while YRC22 and Pseudobutyrivibrio decreased in solids (p < 0.05). Genera with abundances found to be correlated with fermentation products in the liquid included Shuttleworthia, Treponema, Lachnospira, and Schwartzia, which typically have lower relative abundances, showing strong positive correlations with molar proportions (mol%) of propionate, butyrate, and valerate (p < 0.05), and negative correlations with pH and acetate mol% (p < 0.05). Fibrobacter was positively correlated with lactate mol% (p < 0.05). Butyrate mol% exhibited a quadratic increase as molasses increased (p = 0.017), and lactate mol% rose with increased RDP levels (p = 0.042). No treatment effects were detected for pH propionate and valerate mol%; however, we observed a tendency (p = 0.075) for a quadratic effect of molasses treatment on the mol% of acetate. These findings substantiate the pivotal role of diet in shaping rumen microbiota and metabolism, elucidating a nuanced relationship between dietary components, bacterial community structure, and metabolic output. This offers a more detailed understanding of rumen function and the potential for high-precision dietary management in lactating cows.

DISTRIBUTION AND DIVERSITY OF GASTROPODS (MOLLUSCS) IN INTERTIDAL WATERS IN RUPAT SUBDISTRICT, BENGKALIS DISTRICT

This study aims to determine the distribution pattern and diversity of gastropods in the Intertidal Waters of the Rupat Timur District. The research was conducted in February 2022. The research location consisted of 3 stations, each station was placed 3 transects from the highest tide to the lowest tide at different distances. Along the transect lines were placed 3 plots with a size of 3 x 3 m and each plot has a subplot with a size of 1 x 1 m. The method used in this research is the survey method. Parameters measured include gastropod species, distribution patterns, diversity, abundance, relative abundance, and water quality. The results of the study found gastropod species consisting of 9 (nine) families, 12 (twelve) genera, and 13 (thirteen) species. The distribution pattern of gastropods in the research location is clustered with the value of diversity (H') at a moderate level of diversity. Diversity is categorized as moderate. The highest abundance of gastropods was found on the beach of Sukarjo Mesim Village (a station I) with an abundance value of 25,600 ind/ha and the lowest abundance was found on the beach of Teluk Lecah Village (station III) with an abundance value of 11,100 ind/ha, while the highest abundance of gastropods between intertidal subzones was in the upper zone with an abundance value of 20,400 ind/ha and the lowest abundance was in the lower zone with an abundance value of 12,200 ind/ha. The highest relative abundance was Indothais javanica species with a relative abundance value of 18.30%, while the lowest relative abundance was Oliva ornata species with a relative abundance value of 0.85%. Temperature 29-30o C; salinity 28-30 ppt; pH 5-6; DO 5.2-6.4 mg/l. Sediment type in the station I was dominated by mud, station II was dominated by muddy sand and station III was dominated by sand with total sediment organic matter content of 0.46-23.33%.

Microbiota and Resistome Analysis of Colostrum and Milk from Dairy Cows Treated with and without Dry Cow Therapies.

This study investigated the longitudinal impact of methods for the drying off of cows with and without dry cow therapy (DCT) on the microbiota and resistome profile in colostrum and milk samples from cows. Three groups of healthy dairy cows (n = 24) with different antibiotic treatments during DCT were studied. Colostrum and milk samples from Month 0 (M0), 2 (M2), 4 (M4) and 6 (M6) were analysed using whole-genome shotgun-sequencing. The microbial diversity from antibiotic-treated groups was different and higher than that of the non-antibiotic group. This difference was more evident in milk compared to colostrum, with increasing diversity seen only in antibiotic-treated groups. The microbiome of antibiotic-treated groups clustered separately from the non-antibiotic group at M2-, M4- and M6 milk samples, showing the effect of antibiotic treatment on between-group (beta) diversity. The non-antibiotic group did not show a high relative abundance of mastitis-causing pathogens during early lactation and was more associated with genera such as Psychrobacter, Serratia, Gordonibacter and Brevibacterium. A high relative abundance of antibiotic resistance genes (ARGs) was observed in the milk of antibiotic-treated groups with the Cephaguard group showing a significantly high abundance of genes conferring resistance to cephalosporin, aminoglycoside and penam classes. The data support the use of non-antibiotic alternatives for drying off in cows.

Mediation Analysis of Waist Circumference in the Association of Gut Microbiota with Insulin Resistance in Children.

Persistent gut microbiota (GM) imbalance has been associated with metabolic disease development. This study evaluated the mediating role of waist circumference in the association between GM and insulin resistance (IR) in children. This cross-sectional study included 533 children aged between 6 and 12. The anthropometry, metabolic markers, and relative abundance (RA) of five intestinal bacterial species were measured. Path coefficients were estimated using path analysis to assess direct, indirect (mediated by waist circumference), and total effects on the association between GM and IR. The results indicated a positive association mediated by waist circumference between the medium and high RA of S. aureus with homeostatic model assessments for insulin resistance (HOMA-IR) and for insulin resistance adiponectin-corrected (HOMA-AD). We found a negative association mediated by waist circumference between the low and medium RA of A. muciniphila and HOMA-IR and HOMA-AD. Finally, when we evaluated the joint effect of S. aureus, L. casei, and A. muciniphila, we found a waist circumference-mediated negative association with HOMA-IR and HOMA-AD. Waist circumference is a crucial mediator in the association between S. aureus and A. muciniphila RA and changes in HOMA-IR and HOMA-AD scores in children.

Expanding non-invasive approaches for fish-health monitoring: A survey of the epidermal mucous metabolomes of phylogenetically diverse freshwater fish species.

There is a pressing need for more-holistic approaches to fisheries assessments along with growing demand to reduce the health impacts of sample collections. Metabolomic tools enable the use of sample matrices that can be collected with minimal impact on the organism (e.g., blood, urine, and mucus) and provide high-throughput, untargeted biochemical information without the requirement of a sequenced genome. These qualities make metabolomics ideal for monitoring a wide range of fish species, particularly those under protected status. In the current study, we surveyed the relative abundances of 120 endogenous metabolites in epidermal mucus across eight freshwater fish species belonging to seven phylogenetic orders. Principal component analysis was used to provide an overview of the data set, revealing strong interspecies relationships in the epidermal mucous metabolome. Normalized relative abundances of individual endogenous metabolites were then used to identify commonalities across multiple species, as well as those metabolites that showed notable species specificity. For example, taurine was measured in high relative abundance in the epidermal mucus of common carp (Cyprinus carpio), northern pike (Esox lucius), golden shiner (Notemigonus crysoleucas), rainbow trout (Oncorhynchus mykiss), and rainbow smelt (Osmerus mordax), whereas γ-amino butyric acid (GABA) exhibited a uniquely high relative abundance in flathead catfish (Pylodictis olivaris). Finally, hierarchical cluster analysis was used to evaluate species relatedness as characterized by both the epidermal mucous metabolome (phenotype) and genetic phylogeny (genotype). This comparison revealed species for which relatedness in the epidermal mucous metabolome composition closely aligns with phylogenetic relatedness (e.g., N. crysoleucas and C. carpio), as well as species for which these two measures are not well aligned (e.g., P. olivaris and Polyodon spathula). These, and other findings reported here, highlight novel areas for future research with fish, including development of epidermal mucous-based markers for non-invasive health monitoring, sex determination, and hypoxia tolerance.

Synergistic interactions between anammox and dissimilatory nitrate reducing bacteria sustains reactor performance across variable nitrogen loading ratios.

Anaerobic ammonium oxidizing (anammox) bacteria are utilized for high efficiency nitrogen removal from nitrogen-laden sidestreams in wastewater treatment plants. The anammox bacteria form a variety of competitive and mutualistic interactions with heterotrophic bacteria that often employ denitrification or dissimilatory nitrate reduction to ammonium (DNRA) for energy generation. These interactions can be heavily influenced by the influent ratio of ammonium to nitrite, NH4+:NO2-, where deviations from the widely acknowledged stoichiometric ratio (1:1.32) have been demonstrated to have deleterious effects on anammox efficiency. Thus, it is important to understand how variable NH4+:NO2- ratios impact the microbial ecology of anammox reactors. We observed the response of the microbial community in a lab scale anammox membrane bioreactor (MBR) to changes in the influent NH4+:NO2- ratio using both 16S rRNA gene and shotgun metagenomic sequencing. Ammonium removal efficiency decreased from 99.77 ± 0.04% when the ratio was 1:1.32 (prior to day 89) to 90.85 ± 0.29% when the ratio was decreased to 1:1.1 (day 89-202) and 90.14 ± 0.09% when the ratio was changed to 1:1.13 (day 169-200). Over this same timespan, the overall nitrogen removal efficiency (NRE) remained relatively unchanged (85.26 ± 0.01% from day 0-89, compared to 85.49 ± 0.01% from day 89-169, and 83.04 ± 0.01% from day 169-200). When the ratio was slightly increased to 1:1.17-1:1.2 (day 202-253), the ammonium removal efficiency increased to 97.28 ± 0.45% and the NRE increased to 88.21 ± 0.01%. Analysis of 16 S rRNA gene sequences demonstrated increased relative abundance of taxa belonging to Bacteroidetes, Chloroflexi, and Ignavibacteriae over the course of the experiment. The relative abundance of Planctomycetes, the phylum to which anammox bacteria belong, decreased from 77.19% at the beginning of the experiment to 12.24% by the end of the experiment. Analysis of metagenome assembled genomes (MAGs) indicated increased abundance of bacteria with nrfAH genes used for DNRA after the introduction of lower influent NH4+:NO2- ratios. The high relative abundance of DNRA bacteria coinciding with sustained bioreactor performance indicates a mutualistic relationship between the anammox and DNRA bacteria. Understanding these interactions could support more robust bioreactor operation at variable nitrogen loading ratios.

Greywater treatment performance of a pilot-scale membrane bioreactor and characteristics of bacterial biofilm signatures in permeate effluent

Treated greywater has a high potential for water reuse. However, the post-treatment processes of reclaimed greywater may face biofouling problems due to biofilm formation. In the present study, the greywater treatment performance of a pilot-scale membrane bioreactor (MBR) was evaluated, and the effect of a dominant bacterial biofilm growing on the Pall ring media placed in the permeate pipeline was investigated. The MBR was operated for 125 days with a constant hydraulic retention time of 2 days under complete sludge retention. The treatment performance in terms of the levels of organic compounds, ammonium nitrogen, suspended solids, total coliforms, and Escherichia coli was >90 %. During the operation, a high relative abundance (>70 %) of the following bacterial phyla was observed within the MBR and the bacterial biofilm: Proteobacteria, Chloroflexi, Actinobacteria, and Planctomycetes. Furthermore, the following bacterial orders were predominantly observed in the biofilm: Sphingomonadales, Burkholderiales, and Planctomycetes. Acidovorax, Methylibium, Blastomonas, and Planctomyces were the important genera identified in the biofilm. Interestingly, the present study revealed that these bacterial species were predominant and well adapted in treated greywater containing various surfactant and detergent components. Knowledge of the predominant bacterial species in the biofilm could enable to select the appropriate disinfection method and prevent the biofouling of the reverse osmosis (RO) membrane, which can facilitate further application of the MBR-RO process for water reuse.

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.