Higher Relative Abundance Research Articles

Italian ryegrass (Lolium multiflorum L.)-rice (Oryza sativa L.) rotation promotes the nitrogen cycle in the rice rhizosphere through dominant ammonia-oxidizing bacteria

The dominant ammonium bacteria established in different crop rotations are directly related to the conversion and utilization of nitrogen (N) in paddy soil. This study investigated the ammonia oxidation process in the rice rhizosphere of Italian ryegrass (Lolium multiflorum L.)-rice (IRR), celery (Apium graveolens)-rice (CLR) and winter fallow-rice (WFR) rotations in South China through the amoA functional gene analysis based on Miseq high-throughput sequencing platform and qPCR methods. The abundance of amoA gene in IRR was increased by 116.67 % (P < 0.05) and 42.76 % (P > 0.05) compared with CLR and WFR, respectively. Nitrosomonas became the dominant genus in the rhizosphere of IRR, with the highest relative abundance (59.30 %). The contents of soil organic matter, total N and nitrate nitrogen (NO3−-N) in the rice rhizosphere soil in IRR were significantly higher than other two treatments (P < 0.05) by 12.47–14.31 %, 16.88–25.00 %, and 97.48–159.60 %, respectively. Although lower microbial diversity was observed in IRR, the soil fluorescein diacetate hydrolysis enzyme activities and ammonia monooxygenase activities in the rice rhizosphere were higher in IRR than those in CLR and WFR (P < 0.05). Also, the soluble sugar and crude protein of milled rice were highest in IRR among the three rotation treatments (P < 0.05). The ammonia oxidation efficiency of ammonium-oxidizing bacteria was largely dependent on key taxa, such as Nitrosomonas (dominant genus in IRR), rather than the dynamics of AOB community structure. The key amoA-nitrifier taxa of the AOB community developed in IRR are capable of promoting rice production by improving soil N cycle efficiency and reducing the loss of N. Our findings illustrate the regulatory mechanism of IRR on the rice rhizosphere AOB community and reveal the important role of winter ryegrass in promoting soil nitrogen cycling during nutrient transformation of agricultural ecosystems in paddy fields.

Occurrence of putative Culicoides biting midge vectors (Diptera: Ceratopogonidae) inside and outside barns in Germany and factors influencing their activity

BackgroundAfter several years without bluetongue disease, a ruminant illness caused by Culicoides-borne bluetongue virus (BTV), two new autochthonous cases were reported in 2018 in Germany. By contrast, Schmallenberg virus (SBV), another Culicoides-borne virus pathogenic to ruminants, has continuously circulated in Germany since its first emergence in 2011. The disease outbreaks have triggered numerous studies on the biology of the Culicoides vectors, but many ecological details are still obscure.MethodsCulicoides biting midge species were collected with UV-light traps on 10 farms in Germany, with one trap inside and one trap outside barns on each of the farms. Traps were run once a week for 24 h from January to December 2019. Collected biting midges were morphologically identified, counted and statistically evaluated, with a focus on the Obsoletus Group and the Pulicaris Complex of the ceratopogonid genus Culicoides, which are believed to contain the major virus vectors. Temperature and relative humidity recorded at each trap were linked to the quantity of caught Culicoides. Correlations between relative Culicoides abundance and presence of livestock or type of husbandry were also investigated.ResultsA total of 38,886 Culicoides biting midges were trapped, with most of them belonging to the Obsoletus Group (51.0%) and the Pulicaris Complex (38.8%). The majority of captured specimens were collected in traps inside the barns. Obsoletus Group individuals were caught from late January to the last week of December while Pulicaris Complex individuals were captured from the end of March to early December. The lowest average temperatures at which members of the two groups were collected were 10.7 °C and 12.8 °C, respectively. While temperature had a statistically significant effect on the activity of both the Obsoletus Group and the Pulicaris Complex, relative humidity only significantly affected the activity of the latter. The presence of livestock significantly influenced the number of captured Obsoletus Group, but not of Pulicaris Complex specimens. Inside the barns, no statistical difference was found between numbers of caught Obsoletus Group and Pulicaris Complex specimens in livestock holdings with deep litter and manure scraper or slatted floor husbandry systems.ConclusionsThe almost year-round presence of Obsoletus Group biting midges and the demonstrated high relative abundance of other potential Culicoides vector species inside barns suggest a high risk of indoor virus transmission to ruminants should BTV or SBV circulate locally. Appropriate structural, organisational and vector control measures to reduce biting midge exposure should be implemented.Graphical

Comparative analysis of eukaryotic microbial communities associated with Acropora formosa, sediment, and seawater in a coral reef ecosystem of Whale island, Nha Trang bay, Vietnam

In this study, eukaryotic microbial communities associated with coral Acropora formosa and its natural surroundings, sediment and seawater, in a coral reef ecosystem of Whale Island, Nha Trang Bay, Vietnam were investigated. First, genetic material was taken from Acropora formosa’s surface mucus layer (SML) as well as the sediment underneath and seawater above the colonies from four different sampling locations in a coral reef ecosystem. Subsequently, the data were sequenced using 18S rRNA gene amplicon sequencing method. Sequences (reads) were then analyzed in Rstudio version 4.2.0. Bioinfomatic tools such as DADA2 pipeline clustered the sequences into amplicon sequence variants (ASVs), to which the taxonomy was assigned using SILVA 132 database. The majority of the sequences was categorized at the kingdom and phylum levels, but fewer sequences were identified at genus and species level. The visualization of the results revealed changes in abundance and composition of the eukaryotic communities in all samples. The results demonstrated that phylum Dinoflagellata had the highest relative abundance in coral samples. Meanwhile, Ochrophyta was the most prevalent phylum in seawater samples. Notably, after filtering out the sequences with abundance less than 2%, only genus Symbiodinium appeared significantly in coral samples. The composition of samples from coral sampling sites was more consistent. The same was true for samples of seawater, whereas the composition of sediment samples varied more. Alpha and beta diversity indices confirmed that there were significant differences (p &lt; 0.05) in abundance and composition of eukaryotic communities among three different habitats. These findings come as the first effort to explore the diversity of eukaryotic communities in different habitats and could be valuable for further study in functional profiling or metabolic functions of microbial communities in the coral ecosystem.

Remediation of fomesafen contaminated soil by Bacillus sp. Za: Degradation pathway, community structure and bioenhanced remediation

Fomesafen is a diphenyl ether herbicide used to control the growth of broadleaf weeds in bean fields. The persistence, phytotoxicity, and negative impact on crop rotation associated with this herbicide have led to an increasing concern about the buildup of fomesafen residues in agricultural soils. The exigent matter of treatment and remediation of soils contaminated with fomesafen has surfaced. Nevertheless, the degradation pathway of fomesafen in soil remains nebulous. In this study, Bacillus sp. Za was utilized to degrade fomesafen residues in black and yellow brown soils. Fomesafen's degradation rate by strain Za in black soil reached 74.4%, and in yellow brown soil was 69.2% within 30 days. Twelve intermediate metabolites of fomesafen were identified in different soils, with nine metabolites present in black soil and eight found in yellow brown soil. Subsequently, the degradation pathway of fomesafen within these two soils was inferred. The dynamic change process of soil bacterial community structure in the degradation of fomesafen by strain Za was analyzed. The results showed that strain Za potentially facilitate the restoration of bacterial community diversity and richness in soil samples treated with fomesafen, and there were significant differences in species composition at phylum and genus levels between these two soils. However, both soils shared a dominant phylum and genus, Actinobacteriota, Proteoobacteria, Firmicutes and Chloroflexi dominated in two soils, with a high relative abundance of Sphingomonas and Bacillus. Moreover, an intermediate metabolite acetaminophen degrading bacterium, designated as Pseudomonas sp. YXA-1, was isolated from yellow brown soil. When strain YXA-1 was employed in tandem with strain Za to remediate fomesafen contaminated soil, the degradation rate of fomesafen markedly increased. Overall, this study furnishes crucial insights into the degradation pathway of fomesafen in soil, and presents bacterial strain resources potentially beneficial for soil remediation in circumstances of fomesafen contamination.

Bacterial community structure and predicted function in the rhizosphere of wild and cultivated date palms: Effects of Fertilizers on Composition and Functionality

This study investigated bacterial diversity in date palm rhizosphere and assessed the influence of different fertilizers on diversity using metagenomics. A total of 6356 Operational Taxonomic Units (OTUs) and 1164425 sequences were analyzed across 27 samples. The findings revealed variations in microbial community phylogeny among similar cultivars from different farms, except for the Khalas cultivar, suggesting minor influence of genotype on microbial community structure. Wild date palms exhibited more unique OTUs, in contrast, cultivated date palms had a higher number of OTUs and diversity. Moreover, different fertilizer treatments had varying effects on bacterial diversity. For example, organic and bio-organic fertilizers positively influenced specific bacterial groups, including delta-proteobacteria, acidobacteria-Gp3, Anaerolinaea, and Clostridia. Conversely, combining high concentrations of chemical fertilizers with other types did not show significant effects. Classes such as Bacilli, Nitrospira, Deltaproteobacteria, Spartobacteria, and Thermomacrobia exhibited high relative abundances in treatments with high chemical fertilizer concentrations. Our analysis revealed potential pathways related to carbon, nitrogen, phosphorus, phenol, sulfur, and antimicrobial compounds. Interestingly, these pathways and functions varied across different date palm cultivars. Our findings suggest that date palm cultivars shape the rhizosphere by selectively influencing bacterial communities consistently across other locations. These modulated bacterial communities can potentially provide enhanced benefits to the host. Importantly, this study was the first to investigate the soil bacterial diversity of wild date palms, giving valuable insights into the microbial community associated with this specific context.

Causal relationship between gut microbiota and type 2 diabetes: a two-sample Mendelian randomization study.

Studies showed that development of gut microbial dysbiosis has a close association with type 2 diabetes (T2D). It is not yet clear if there is a causal relationship between gut microbiota and T2D. The data collected from the published genome-wide association studies (GWASs) on gut microbiota and T2D were analyzed. Two-sample Mendelian randomization (MR) analyses were performed to identify causal relationship between bacterial taxa and T2D. Significant bacterial taxa were further analyzed. To confirm the findings' robustness, we performed sensitivity, heterogeneity, and pleiotropy analyses. A reverse MR analysis was also performed to check for potential reverse causation. By combining the findings of all the MR steps, we identified six causal bacterial taxa, namely, Lachnoclostridium, Oscillospira, Roseburia, Ruminococcaceae UCG003, Ruminococcaceae UCG010 and Streptococcus. The risk of T2D might be positively associated with a high relative abundance of Lachnoclostridium, Roseburia and Streptococcus but negatively associated with Oscillospira, Ruminococcaceae UCG003 and Ruminococcaceae UCG010. The results of MR analyses revealed that there were causal relationships between the six different genera and T2D. And the reverse MR analysis did not reveal any evidence of a reverse causality. This study implied that Lachnoclostridium, Roseburia and Streptococcus might have anti-protective effect on T2D, whereas Oscillospira, Ruminococcaceae UCG003 and Ruminococcaceae UCG010 genera might have protective effect on T2D. Our study revealed that there was a causal relationship between specific gut microbiota genera and T2D.

A high-concentrate diet induces colonic inflammation and barrier damage in Hu sheep

Long-term feeding of a high-concentrate diet can induce subacute ruminal acidosis (SARA) in ruminants, which further leads to systemic inflammatory response. However, few studies have examined the effects of feeding a high-concentrate diet on the hindgut of ruminants. The purpose of this study was to investigate the effects of a high-concentrate diet on the composition of gut microbiota in colonic contents, inflammatory response, and barrier damage in the colon tissue of ruminants. A total of 12 healthy multiparous lactating Hu sheep were randomly allotted into the following 2 groups: a high-concentrate (HC) group (concentrate:forage = 7:3) and a low-concentrate (LC) group (concentrate:forage = 3:7). All sheep were fitted with ruminal fistulas. The formal feeding experiment lasted for 8 wk. After the feeding experiment, rumen fluid, portal vein blood, hepatic vein blood, colonic contents, and colon tissue samples were collected. The results showed that feeding the HC diet induced SARA in Hu sheep and significantly reduced pH in the colonic contents. The abundances of Firmicutes, Verrucomicrobiota, and Actinobacteriota decreased significantly, whereas those of Bacteroidota, Spirochaetota, and Fibrobacterota significantly increased in colonic contents. At the genus level, the relative abundances of 29 genera were significantly altered depending on the different type of diets. Analysis of the 10 bacterial genera with high relative abundance revealed that feeding the HC diet significantly reduced the abundance of UCG-005, Christensenellaceae R-7 group, UCG-010-norank, Monoglobus, [Eubacterium] coprostanoligenes group_norank, and Alistipes, whereas the abundances of Rikenellaceae RC9 gut group, Treponema, Bacteroides, and Prevotella increased. Compared with the LC group, feeding the HC diet significantly increased the concentration of LPS in rumen fluid, portal vein blood, hepatic vein blood, and colonic contents, and significantly upregulated the mRNA expression levels of proinflammatory cytokines in colon tissue, including TNF-α, IL-1β, IL-6, and IL-8, indicating the occurrence of inflammatory response in the colon tissue. In addition, the structure of colonic epithelial cells was loose, the intercellular space became larger, epithelial cells were exfoliated, and the mRNA and protein abundances of ZO-1, occludin, claudin-1, claudin-3, and claudin-4 were significantly decreased in the HC group, which was consistent with the results of immunohistochemistry. Furthermore, feeding the HC diet increased the ratios of DNA methylation and chromatin compaction in the promoter regions of occludin and claudin-1, which in turn inhibited their transcriptional expression. Therefore, the present study demonstrated that feeding an HC diet induced SARA in Hu sheep, altered the composition and structure of the microbial community in the colonic contents, induced an inflammatory response, and disrupted the intestinal mucosal barrier in the colonic tissue.

Effect of different types of volatile fatty acids on the performance and bacterial population in a batch reactor performing biological nutrient removal

Different ratios of four volatile fatty acids (VFAs) were used as the primary feed to a laboratory scale biological nutrient reactor during four operational stages. The reactor performed efficiently over 500 days of operation with over 90% dissolved phosphorus and over 98% ammonium-nitrogen (NH4+-N) removal. Through in the first experimental phase, acetate and propionate were present in a significant proportion as carbon sources, the relative abundance of Candidatus Accumulibacter, a potential polyphosphate accumulating organism, increased from 10% to 57% and the Defluviicoccus genus, a known glycogen accumulating organism (GAO), decreased from 41% to 5%. Further tests indicated the presence of denitrifying phosphorus accumulating organisms (DPAO) belonging to Clade IIC, that could use nitrite as the electron acceptor during P-uptake. In general, VFAs favored the increase of the genus Defluviicoccus and Candidatus Accumulibacter. High relative abundance of Defluviicoccus did not affect the stability and the performance of the BNR process.

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 &amp;lt; 0.05). Of the 30 genera with the highest relative abundance, 26 differed by digesta fraction (p &amp;lt; 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 &amp;lt; 0.05), and CF231, YRC22, Clostridium, Desulfovibrio, BF311, and Oscillospira increased in solids (p &amp;lt; 0.05). In contrast, at higher RDP levels, Succiniclasticum increased while YRC22 and Pseudobutyrivibrio decreased in solids (p &amp;lt; 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 &amp;lt; 0.05), and negative correlations with pH and acetate mol% (p &amp;lt; 0.05). Fibrobacter was positively correlated with lactate mol% (p &amp;lt; 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.