Non-metric Multidimensional Scaling Plots Research Articles

Diversity and distribution of small-sized planktonic ciliate communities in the East China Sea

Ciliates are an important ecological component in the microbial food web, but few studies have been conducted on the spatial distribution of small-sized planktonic ciliate communities in the East China Sea (ECS). Investigating ciliate communities using conventional morphological approaches is particularly difficult for the small, fragile, and naked species. Therefore, we applied DNA metabarcoding analysis to explore the spatial pattern of small-sized planktonic ciliate community structure within the surface, deep chlorophyll maximum (DCM), and bottom layers. Results showed the cosmopolitan species, Leegaardiella sp., was dominant and widespread in the ECS. The relative abundance of the mixotrophic family Tontonnidae decreased in the deeper layer. We characterized water masses of the ECS using environmental variables. In nano-sized ciliate communities, non-metric multidimensional scaling (NMDS) plots revealed a correlation with temperature, salinity, density, and depth. The circulation patterns were similar to cluster analysis results, suggesting that hydrographic conditions shaped small-sized ciliate community composition.

Can artificially induced habitat complexity alter macroinvertebrates diversity? A case study from a freshwater wetland ecosystem

Habitat complexity can enhance the resilience of wetlands against environmental stressors such as extreme weather events, pollution, and habitat loss. The introduction of artificial induced complexity (AIC) can play a significant role in reshaping the macroinvertebrate communities within wetland ecosystems by enhancing habitat quality in protected areas. Therefore, this study was designed to examine the variation of macroinvertebrates community structure in artificially induced complex sanctuary site (SS), partially protected (PP) and open sites (OS) from July 2019-April 2020. AIC in the sanctuary sites was established through the installation of cemented hexapods and ring pipes. Over the study period, a total of 665 macroinvertebrates were gathered, with 55.55% originating from SS, 31.14% from PP, and 18.21% from OS sites. The community consists mainly of Lymnaea acuminatatea and Tubifex tubifex, with the most abundant species being Limnodrillus hoffmeisteri and Branchiura sowerbyi. A notable positive impact of AIC was evident in the increased total abundance and diversity indices of macroinvertebrate communities. The Analysis of Similarity (ANOSIM) revealed significant distinctions in community structures among various intervention types, which was further corroborated by a non-metric multidimensional scaling (nMDS) plot. Similarity of Percentage Analysis (SIMPER) highlighted that Limnodrillus hoffmeisteri made the most significant contribution to the dissimilarity observed among the different intervention types. Canonical Correspondence Analysis (CCA) revealed a close association between the structure of the macroinvertebrate community and three key ecological factors: periphyton biomass, macrophyte cover, and sediment properties. These findings could offer a more effective approach for managers and policymakers engaged in the conservation of macroinvertebrates and the sustainable management of fisheries resources within wetland ecosystems.

Medication Trends in the Military: A Comparative Analysis of Prescribing Patterns Among Service Members Seen by a Pharmacist and Implications for Medical Readiness.

Medications play a critical role supporting the health of military service members. Little is known about the broad use of medications prescribed to this population. Active duty service members (ADSMs), while often younger and having fewer diagnosed comorbid conditions, face unique health challenges that benefit from pharmacotherapy. Understanding prescribing patterns is instrumental to illuminate potential areas for research and to guide education so that military health care professionals can maintain competency, improve outcomes, and support medical readiness. This study aimed to characterize commonly dispensed medications among ADSMs and to compare these prescriptions with those of the general population. A retrospective, cross-sectional analysis using data extracted contained in the Military Health System Information Platform focused on ADSMs who consulted with a clinical pharmacist during the 2019 fiscal year. Descriptive statistics were used to summarize patient and prescription data. The 100 most frequently prescribed medications and 20 most frequently prescribed therapeutic classes were identified. Analyses were performed using Statistical Analysis System (SAS) software, and a non-metric multidimensional scaling plot was generated in R to illustrate the relationships between the 20 most frequently used therapeutic classes and the branches of service. The study analyzed 719,788 prescriptions for 30,012 service members, revealing a high prescription rate for pain, inflammation, and psychiatric condition treatments. Antidepressants and nonsteroidal anti-inflammatory drugs were among the most commonly prescribed across all military branches. Some medication uses varied, which may indicate distinct needs within different service branches. Understanding medication patterns among ADSMs may be able to help health care professionals proactively address pharmacological challenges and optimize pharmaceutical use in this unique population. This knowledge can also aid in the development of training modules focused on medication side effects, interactions, counseling, and implications on military deployment for the most commonly used medications. Future examination into prescribing cascades and medication use related to proton-pump inhibitors, docusate, benzonatate, and muscle relaxants may identify opportunities to provide better care or lower cost.

The effects of bee species and vegetation on the antioxidant properties of honeys produced by Afrotropical stingless bees (Hymenoptera, Apidae, Meliponini)

Stingless bee honey is widely utilized as a traditional medicine in tropical and subtropical regions. The rich diversity of stingless bees and floral resources in the African tropics presents an opportunity for the production of honeys with diverse therapeutic properties. This study investigated the influence of bee species and vegetation on the antioxidant properties of stingless bee honey. Honey samples were collected from six species of Afrotropical stingless bees in six different vegetation zones of Tanzania, and tested for phytochemical composition and antioxidant activity. Our findings demonstrate that the antioxidant properties of stingless bee honey were influenced by both bee species and vegetation, with the former exhibiting a stronger effect. Honeys produced by different stingless bee species varied significantly in all of the assayed parameters, whereas honey samples from different vegetation zones differed in 80% of the parameters. Further, there was a clear separation of honey samples based on bee species on the non-metric multidimensional scaling (NMDS) and principal component analysis (PCA) plots which suggests that the antioxidant properties can be used as markers for discriminating honeys produced by different bee species. The studied stingless bee species across different vegetation zones produced honeys with remarkable phenolic content (46.80–365.17 mg GAE/100 g), flavonoid content (27.49–210.83 mg QE/100 g), vitamin C (7.42–60.50 mg/100 g), radical scavenging activity (32.75–92.50%) and ferric reducing antioxidant power (68.11–221.23 μmol Fe (II)/100 g). Stingless bee honey presents a promising niche for pharmaceutical research and innovation, particularly for Dactylurina schmidti honey which demonstrated exceptional levels of phytochemicals and antioxidant activity. We encourage future studies to investigate the biologically active components in honeys produced by Afrotropical stingless bees, paving the way for potential applications of stingless bee honey in clinical therapy.

A registry-based population study of the HLA in Québec, Canada.

As part of the worldwide effort to better characterize HLA diversity in populations, we have studied the population of Québec in Canada. This province has been defined by a complex history with multiple founder effects and migration patterns. We analyzed the typing data of 3806 individuals registered in Héma-Québec's Registry, which covered most administrative regions in Québec. Typing information was resolved at the second field level of resolution by next-generation sequencing (NGS) or by Sanger sequencing. We used the HLA-net.eu GENE[RATE] tools to estimate allele and two-locus haplotype frequencies for HLA-A, -B, -C, -DRB1, -DQB1, and -DPB1, as well as Hardy-Weinberg equilibrium (HWE), selective neutrality, and linkage disequilibrium. The chord genetic distance was also calculated between administrative regions and was visualized using non-metric multidimensional scaling (NMDS) analysis. While most individual regions were in HWE, HWE was rejected for the province considered as a whole. Some regions exhibited signatures of selection, mostly toward an excess of heterozygotes. Allele and haplotype frequencies revealed outlier regions that strongly differed from the other regions. NMDS plots also showed differences between regions. The administrative regions of the province of Québec displayed heterogeneity in their HLA profiles. This heterogeneity was attributable to differing allele and haplotype specificities by region. In particular, regions 02-Saguenay-Lac-Saint-Jean and 01-Bas-St-Laurent diverged from the rest of the regions. The urban regions 06-Montréal and 13-Laval were very diversified in their HLA profiles. Together, these results will help optimize donor recruitment strategies in Québec.

Assessing the Changes in Protein Content During the Ensilage of the Indian Mackerel (Rastrelliger kanagurta) by Biological Method

Fish silage is a liquefied product resulting from tissue hydrolysis and the richness of the silage is characterized by its nutritional profile comprising of proteins, amino acids, and fats. For the production of fish silage of high nutritional value, a precise assessment of the degree of hydrolysis, particularly proteolysis becomes a paramount importance. The goal of this study is to assess the changes in protein content in fish silage prepared from the Indian mackerel (Rastrelliger kanagurta) waste using 10% (v/w) sugarcane molasses, during 8 days of fermentation (DoF). The resultant ensiled product was evaluated for changes in titratable acidity, nutrients, total protein, total carbohydrate, total lipids content, and amino acid composition. Altogether, 17 types of amino acids were identified. Concentrations of total amino acids (TAAs, 15.627 ± 0.03 mg/g) and free amino acids (5.556 ± 0.08 mg/g) peaked at the end of 6 DoF with the predominance of histidine, arginine, alanine, asparagine, aspartic acid, and glutamic acid. Results of the non-metric multidimensional scaling (nMDS) plots and one-way analysis of similarities (ANOSIM) test indicated significant differences in the composition of TAAs at different DoF were discernible (nMDS, stress 0.03162, one-way ANOSIM R = 1; p < 0.0001). Similarity percentage (SIMPER) analysis indicated that the maximum content of amino acids (TAA and FAA) were released in silage during 4–6 DoF. A significant difference was observed in concentrations of most amino acids except cysteine, serine, and tryptophan (ANOVA, p < 0.05) at 2, 4, 6 and 8 DoF. Considering the vital role played by amino acids in providing resistance to plant pathogens as well as contributing to animal nutritional supplements, the results of the present study are highly noteworthy.

Spatial and temporal environmental heterogeneity induced by internal tides influences faunal patterns on vertical walls within a submarine canyon

Vertical walls of submarine canyons represent features of high conservation value that can provide natural areas of protection for vulnerable marine ecosystems under increasing anthropogenic pressure from deep-sea trawling. Wall assemblages are spatially heterogeneous, attributed to the high environmental heterogeneity over short spatial scales that is a typical feature of canyons. Effective management and conservation of these assemblages requires a deeper understanding of the processes that affect faunal distribution patterns. Canyons are recognised as sites of intensified hydrodynamic regimes, with focused internal tides enhancing near-bed currents, turbulent mixing and nepheloid layer production, which influence faunal distribution patterns. Faunal patterns also respond to broad-scale hydrodynamics and gradients in water mass properties (e.g. temperature, salinity, dissolved oxygen concentration). Oscillating internal tidal currents can advect such gradients, both vertically and horizontally along a canyon's walls. Here we take an interdisciplinary approach using biological, hydrodynamic and bathymetry-derived datasets to undertake a high-resolution analysis of a subset of wall assemblages within Whittard Canyon, North-East Atlantic. We investigate if, and to what extent, patterns in diversity and epibenthic assemblages on deep-sea canyon walls can be explained by spatial and temporal variability induced by internal tides. Vertical displacement of water mass properties by the internal tide was calculated from autonomous ocean glider and shipboard CTD observations. Spatial patterns in faunal assemblage structure were determined by cluster analysis and non-metric Multi-Dimensional Scaling plots. Canonical Redundancy Analysis and Generalised Linear Models were then used to explore relationships between faunal diversity and assemblage structure and a variety of environmental variables. Our results support the hypothesis that internal tides influence spatial heterogeneity in wall faunal diversity and assemblages by generating both spatial and temporal gradients in hydrodynamic properties and consequently likely food supply.

Assessment of water quality and its effect on prawn abundance in three tributaries of Shiwalik rivers: Chenab and Ravi of Jammu, India—a case study

The freshwater rivers from Shiwalik Himalayas have abundant prawn resources of high economic value and play a major role in the livelihood of local fishermen. The present study aimed to determine the variation in prawn abundance explained by changes in water quality among three different streams (Gho Manhasa stream, Chadwal stream and Nagri stream). The highest abundance of prawns was found in the Gho Manhasa during the premonsoon season and lowest in the Chadwal stream during the monsoon season. Chadwal stream witnessed maximum anthropogenic activities resulting in the decline of the water quality affecting prawn fauna. Cluster analysis based on similarity in terms of prawn abundance revealed that the Chadwal stream is different from the other two streams whereas non-metric multidimensional scaling plot based on species abundance corresponding to different seasons and physiochemical parameters showed the water quality of the monsoon season of the Chadwal stream to be extremely different. Principal component analysis showed clear separation across various sites and seasons based on physicochemical parameters. Karl Pearson correlation coefficient and canonical correspondence analysis indicated that the turbidity, total dissolved solids, nitrate, chloride, calcium, magnesium and dissolved oxygen are significant parameters influencing the abundance of prawns. The population of Macrobrachiumdayanum and Macrobrachiumkistnense was very less in the Chadwal stream owing to unfavorable physicochemical parameters. Therefore, conservation measures are suggested which should be immediately implemented before the streams witness a further decline in their populations.

Fish diversity and assemblage in the Batticaloa lagoon, Sri Lanka.

The Batticaloa Lagoon (Sri Lanka's third-largest brackish waterbody) has suffered habitat degradation and water quality deterioration during the past 30 years due to various anthropogenic activities. Despite Sri Lanka having 40 lagoons, inventories on the lagoon ichthyofauna are rather meagre and data on fish diversity and assemblages are scarce. An assessment of fish diversity is essential to maintain the ecological stability and lagoon fisheries. This study examined the fish fauna of the Batticaloa lagoon considering the northern and southern regions of the lagoon and various depths through a 3-year survey (2017-2019) and documented the dominant and rare fish species. In addition, biodiversity measures, species assemblages and the role of environmental parameters on the distribution of fishes were documented. Various diversity indices (the Margalef richness index, the Shannon-Weiner diversity index, Pielou's evenness index, the dominance index, the taxonomic diversity index, the average taxonomic distinctness index and the total taxonomic distinctness index) were calculated. Analysis of similarities (ANOSIM) was used to examine the seasonal and regional differences in the fish assemblages. The survey showed the occurrence of 96 species belonging to 40 families and 11 orders. Ambassis gymnocephalus was the most abundant fish species (8.7% of the total number of fishes collected) followed by Etroplus suratensis (6.8%), Arius maculatus (6.1%), Gerres filamentosus (5.3%), Oreochromis niloticus (4.6%) and Gerres abbreviates (3.9%). Dasyatis uarnak (0.02%), Acanthurus gahhm (0.03%), Alectis ciliaris (0.04%) and Crossorhombus valderostratus (0.08%) were considered as rare species which constitute less than 0.1% of the total while D. uarnak was considered a doubletons species (represented twice in the whole sample of 16 stations). Two types of species assemblages, one in the northern region and one in the southern region, were evident in a dendrogram (Based on the samples were collected on each region dendrogram were plotted with respect to sites then finally dendrogram of one region pratly connected by other region) based on sample composition similarity estimated with a Bray-Curtis matrix and nonmetric multidimensional scaling plots. The Bray-Curtis dissimilarity was 59.03% between the two regions, indicating statistically significant differences in assemblages (ANOSIM R 0.801; P < 0.01). The northern region of the lagoon had a higher number of species, density, Margalef richness, Pielou's evenness, Shannon-Wiener diversity, taxonomic diversity, taxonomic distinctness and total taxonomic distinctness compared to the southern region. The northern region showed significantly higher levels of salinity and dissolved oxygen (DO) and the southern region higher temperature, turbidity, phosphates and nitrates. The best subset of biota and environmental variables [BEST(BIO-ENV)] test showed a significant relationship between fish assemblage and environmental parameters. Distance-based linear model analysis showed a significant relationship between fish assemblage and the environmental parameters salinity, temperature, pH and DO. The sequential test of this analysis showed the environmental parameters to explain about 74.9% (R2 ) of the total variation. The bioenvironmental model developed was found to be appropriate. Thirteen species were found to be influential as they explained the overall fish distribution pattern with a Spearman rank correlation of 0.951. Ten groups of coherent species were also identified in the study area. In stations having anthropogenic activities, the fish diversity was low. The fish fauna of the Batticaloa lagoon should be monitored periodically to protect the fishery resources here. An understanding of the role that environment plays in structuring the fish assemblage in the Batticaloa lagoon and locations with critical habitats will be of great importance in the conservation and management of fishery resources in this lagoon. However, as monitoring only the dominant species may fail to pick up on important impacts affecting the less common species, it should be done using diversity indices and rare fish species. Monitoring is imperative in view of the livelihood of the fishers this lagoon supports and the health of the local people, as fish is a healthy food. The fishery resources of this lagoon must be protected for posterity with appropriate management measures.

Amplicon-based assessment of bacterial diversity and community structure in three tropical forest soils in Kenya

Forest soils provide a multitude of habitats for diverse communities of bacteria. In this study, we selected three tropical forests in Kenya to determine the diversity and community structure of soil bacteria inhabiting these regions. Kakamega and Irangi are rainforests, whereas Gazi Bay harbors mangrove forests. The three natural forests occupy different altitudinal zones and differ in their environmental characteristics. Soil samples were collected from a total of 12 sites and soil physicochemical parameters for each sampling site were analyzed. We used an amplicon-based Illumina high-throughput sequencing approach. Total community DNA was extracted from individual samples using the phenol-chloroform method. The 16S ribosomal RNA gene segment spanning the V4 region was amplified using the Illumina MiSeq platform. Diversity indices, rarefaction curves, hierarchical clustering, principal component analysis (PCA), and non-metric multidimensional scaling (NMDS) analyses were performed in R software. A total of 13,410 OTUs were observed at 97% sequence similarity. Bacterial communities were dominated by Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, and Acidobacteria in both rainforest and mangrove sampling sites. Alpha diversity indices and species richness were higher in Kakamega and Irangi rainforests compared to mangroves in Gazi Bay. The composition of bacterial communities within and between the three forests was also significantly differentiated (R = 0.559, p = 0.007). Clustering in both PCA and NMDS plots showed that each sampling site had a distinct bacterial community profile. The NMDS analysis also indicated that soil EC, sodium, sulfur, magnesium, boron, and manganese contributed significantly to the observed variation in the bacterial community structure. Overall, this study demonstrated the presence of diverse taxa and heterogeneous community structures of soil bacteria inhabiting three tropical forests of Kenya. Our results also indicated that variation in soil chemical parameters was the major driver of the observed bacterial diversity and community structure in these forests.

Vegetation Changes Following Large-scale Fence Removal Across a Protected Area Network Within the Kruger to Canyons Biosphere Reserve, South Africa

In the early 1990’s, reserves adjacent to Kruger National Park (KNP) removed their fences to create a continuous landscape within the Kruger to Canyons Biosphere Reserve. Understanding how these interconnected multi-management systems responded to changes in environmental factors and management regimes can help to maintain natural large-scale landscape heterogeneity and ecological resilience. Our objective was to analyze remote sensing-derived vegetation metric changes between the different management types pre- and post-fence removal. The study area included fourteen reserves and the central section of KNP. We calculated the residuals between TIMESAT-derived metrics (from AVHRR NDVI time series) and rainfall to analyze changes in vegetation from 1985 to 2006. We then compared vegetation-rainfall residuals between different management types pre- and post-fence removal using mean–variance plots, nonmetric multidimensional scaling plots, and permutational multivariate analysis of variance to statistically identify and analyze changes. All management types experienced increased greenness. Reserves that removed their fences had greater changes in vegetation post-fence removal compared to reserves that remained fenced and KNP. Our findings suggest managers may need to address landscape changes by implementing management regimes such as reducing artificial surface water to counterbalance increased grazing pressure as a result of increased animal mobility across artificially created resource gradients. Habitat connectivity within and between protected area networks can be achieved by removing fences across adjacent conservation areas thus potentially increasing ecological resilience, which is vital to effective long-term conservation.

Regulator Of G Protein Signaling 14 Disruption Affects The Gut Microbiota And Metabolome In Mice

The gut microbiota is linked to brown adipose tissue (BAT), but the mechanisms and microbes facilitating BAT production or function are unknown. A novel mouse model containing a gene knock-out of regulator of G protein signaling 14 (RGS14 KO) has increased BAT. Our early studies found distinct microbes in RGS14 KO mice and BAT-specific metabolites. PURPOSE: To identify key gut microbial species and uncover BAT-specific metabolites in RGS14 KO mice. Further, we aim to identify and associate metabolites produced in specific tissue samples with these key gut microbes. METHODS: Twenty-two mice (N = 13 RGS14 KO, N = 9 Wild type (WT)) were used to identify predominant microbes and metabolites. Gut microbiota profiles were obtained by sequencing bacterial ribosomal operons. Metabolomics used ultra-high performance liquid chromatography to evaluate polar and nonpolar untargeted metabolites in fecal, cecal, brain, and BAT samples. Microbiome analysis used Kulczynski distance to compare WT to RGS14 KO reads in two-dimensional non-metric multidimensional scaling (NMDS) plots. Two-tailed t-tests were used to compare WT and RGS14 KO metabolite means (p < 0.05). MetaboAnalyst 5.0 was used to identify significant metabolite pathways in tissue samples and generate pathway plots. RESULTS: Approximately 500 k rRNA reads post QA/QC ((84% identify; >1000 bp alignment) were obtained from all samples by MegaBlast. NMDS plots showed significant bacterial community differences (Genus: p = 0.035; species: p = 0.028; strain: p = 0.037) between WT and RGS14 KO mice. Specifically, RGS14 KO mice housed two unique strains of Akkermansia muciniphilia (A. muciniphilia BIOML-A22 and A. muciniphilia AN78) while WT animals contained A. muciniphilia EB-AMDK-1. Untargeted metabolomics identified 82 significantly different (p < 0.05) unique metabolites were between RGS14 KO and WT mice in one of the four samples. Specifically, RGS14 KO animals had significantly higher levels of G6P, glycyl-l-proline, glyercophosphocholine, isoleucine, pipecolic acid, thymidine, UDP-D-glucose, malate, leucic acid, NADP+, and guanosine in BAT compared to WT animals. CONCLUSION: The gut microbiome differs between RGS14 KO and WT mice from genus to strain level. Unique metabolites found in RGS14 KO BAT may be linked to BAT function. Supported by ONR Grant 826640

Metagenomic Analysis of Urban Wastewater Treatment Plant Effluents in Tokyo.

PurposeUrban wastewater treatment plant (WWTP) effluents, even with proper treatment, may cause antimicrobial resistance (AMR) burden, with a high frequency of acquired antimicrobial resistance genes (ARGs). The dissemination of ARGs into the environment increases the risk of infectious diseases; however, there is little direct evidence regarding their epidemiological effects. This study aimed to assess effluents from urban WWTPs around the Tama River and Tokyo Bay using metagenomic analysis of (AMR) genes (ARGs) and heavy-metal resistance genes.MethodsMetagenomic DNA-seq analysis of water samples and resistome analysis were performed.ResultsThe most prevalent ARG was the sulfonamide resistance gene, sul1, followed by the quaternary ammonium compound resistance gene, qacE, suggesting that basic gene sets (sul1 and ∆qacE) in the class 1 integrons are the predominant ARGs. The aminoglycoside resistance genes, aadA and aph, and macrolide resistance genes, msr(E) and mph(E), were the predominant ARGs against each antimicrobial. blaOXA and blaGES were frequently detected, whereas the blaCTX-M cluster was faintly detected. Non-metric multidimensional scaling plot analysis and canonical correspondence analysis results suggested that marked differences in ARGs could be involved in the seasonal differences; qnrS2, aac(6’)-Ib, and mef(C) increased markedly in summer, whereas msr(E) was more frequently detected in winter. Heavy-metal (Hg and Cu) resistance genes (HMRGs) were significantly detected in effluents from all WWTPs.ConclusionWe characterized a baseline level of the environmental ARG/HMRG profile in the overall community, suggesting that environmental AMR surveillance, particularly in urban WWTPs, is a valuable first step in monitoring the AMR dissemination of bacteria from predominantly healthy individuals carrying notable ARG/Bs.

Effects of high-grain diet feeding on mucosa-associated bacterial community and gene expression of tight junction proteins and inflammatory cytokines in the small intestine of dairy cattle

The objective of this study was to investigate changes in the composition of mucosa-associated bacterial community, the morphology of the small intestinal epithelia, and the gene expressions of junction proteins and inflammatory cytokines in the small intestines of dairy cattle fed a high-grain (HG) diet. A total of 12 ruminally cannulated Holstein cows in mid-lactation were randomly fed either a conventional (CON) diet (40% concentrate, dry matter basis) or an HG diet (60% concentrate, dry matter basis) for 4 wk. At the end of the feeding trial, all the cows were slaughtered and then examined for changes in the small intestinal mucosa-associated bacterial communities using 16S full-length amplicon sequencing. Furthermore, the gene expression of tight junction proteins and inflammatory cytokines in the small intestinal epithelium were studied using real-time quantitative PCR. The results of nonmetric multidimensional scaling plots showed that an HG diet altered the composition of mucosa-associated bacterial communities in the jejunum and ileum. The HG feeding only increased the numbers of operational taxonomic units in the mucosa-associated bacterial community in the jejunum. At the genus level, the HG diet increased the abundance of uncultured Succinivibrionaceae and Lachnospiraceae incertae sedis in the duodenal mucosa, whereas the proportions of Veillonella and Selenomonas increased in the jejunal mucosa. Compared with the CON group, the proportions of Acetitomaculum in both the jejunal and the ileal mucosa were higher in the HG group. Analysis via PICRUSt2 (version 2.2.0-b) suggested that the HG diet increased the abundance of genes related to biodegradation of xenobiotics in the jejunal mucosa and the abundance of genes related to immune disease in the ileal mucosa. Additionally, the group fed an HG diet had higher concentrations of lipopolysaccharides in the jejunal and ileal digesta. The HG feeding caused a downregulation of the mRNA expression of occludin and ZO-1 in the jejunal epithelium, as well as of claudin-1, claudin-4, and ZO-1 in the ileal epithelium. Moreover, the HG diet caused an increase in the mRNA expression of IL-1β, IL-2, and IFN-γ in the jejunal epithelium, but a higher expression of IL-2 and IFN-γ in the ileal epithelium. Correlation analysis revealed that the alteration of lipopolysaccharide levels and mucosa-associated bacterial community might partly contribute to changes in the expression of the epithelial cytokines in the jejunum and ileum during HG feeding. These findings suggest that microbiota residing in the small intestine provide essential health benefits to host dairy cattle.

Macroinvertebrate Assemblages along the Longitudinal Gradient of an Urban Palmiet River in Durban, South Africa.

Simple SummaryRivers are the most threatened ecosystems globally. However, much attention has been directed to natural rivers as urban streams are regarded as unnatural with poor capacity to provide ecosystem services. This study was carried out to explore the capacity of an urban Palmiet River to provide refuge for aquatic biota and the importance of solid wastes in providing habitat for macroinvertebrates in severely disturbed urban rivers. The water was found to be of good quality in the upper reach/headwaters and polluted in the industrial area. However, the river showed the ability to self-purify as the water showed some improvement as it flows downstream. Various sensitive and tolerant groups of macroinvertebrates were found along the river. Although the current condition of the river can still support biodiversity and the functioning of the river, it is unclear if the system could endure further disturbance. Some sites with good-quality water showed low or absence of sensitive organisms due to poor habitat. It is evident that macroinvertebrate assemblages are influenced by the water quality and availability of physical habitat, and solid wastes may provide additional habitat in severely disturbed streams. These findings attest that urban river functioning does not differ from that of a natural river, and it should be appreciated as it provides important ecosystem services for local communities.Urban rivers are regarded as unnatural because they drain catchments characterized by impervious surfaces. The present study explored macroinvertebrate communities in relation to water and habitat quality along the longitudinal gradient of an urban Palmiet River in Durban, South Africa. Sampling was conducted across six sites along the river. The water quality has shown a significant variation (ANOVA, p < 0.05) across six sites. Good-quality water was observed at Site 6, whereas Site 5 exhibiting hypertrophic condition. Sites 4 to 1 were all eutrophic; however, nutrient levels showed to decrease from Site 4 down to Site 2 and increased again at Site 1. A similar trend was observed for habitat quality, with Site 6 showing excellent and Site 5 exhibited poor habitat. Coinciding with water and habitat quality, macroinvertebrate diversity and abundance showed significant differences across six sites. Sensitive palaemonids, notonemourids, and amphipods were only observed in the headwaters and have contributed over 50% of the variation in abundance between Site 6 and other sites. The non-metric multidimensional scaling (NMDS) plot has also shown clear discrimination (MANOVA, p < 0.001) for the Average Score Per Taxon (ASPT) across the six sites. Macroinvertebrate communities have shown a clear association between water and habitat quality. These findings affirm the ecological importance of urban rivers as they provide refuge to aquatic biodiversity, with anthropogenic litter providing additional habitats for other taxa. Despite the current conditions supporting biodiversity and the functioning of the river, it is unclear if the system could endure further disturbance.

Metagenomics Insights Into the Microbial Diversity and Microbiome Network Analysis on the Heterogeneity of Influent to Effluent Water.

Sanitizing the water sources of local communities is important to control the spread of microbial resistance genes, especially those for water-borne illnesses. The activities of antibiotic resistance gene (ARG)-host pathogens pose a threat to public health, and it has been estimated that the infection will lead up to 10 million deaths globally by the year 2050. Hence, in this study, we aim to analyze the efficiency of our municipal wastewater treatment plant (WWTP) process in producing pathogen-free water by investigating the microbial composition between influent and effluent water sites. Shotgun metagenomics sequencing using the Illumina platform was performed on the influent and effluent samples of six different WWTP sites located in Johore, Malaysia. After raw data pre-processing, the non-redundant contigs library was then aligned against BLASTP for taxonomy profiling and the Comprehensive Antibiotic Resistance Database for ARG annotation. Interestingly, the alpha-diversity result reported that effluent site samples showed higher abundance and diverse heterogeneity compared to the influent site. The principal component analysis (PCA) and non-metric multidimensional scaling (NMDS) plots also suggested that effluent sites showed high variation in the genetic material due to loosely clustered sample plots, as compared to the tightly clustered influent samples. This study has successfully identified the top three abundant phyla in influent—Proteobacteria, Firmicutes, and Bacteroidetes—and effluent—Proteobacteria, Actinobacteria, and Bacteroidetes—water. Despite the overlap within the top three abundant phyla in influent and effluent sites (Proteobacteria and Bacteroidetes), the ARG composition heat map and drug class phenotype plot bar exhibits a general trend of a downward shift, showing the efficiency of WWTP in reducing opportunistic pathogens. Overall, it was demonstrated that our municipal WWTP efficiently eliminated pathogenic microbes from the influent water before its total discharge to the environment, though not with the total elimination of microorganisms. This metagenomics study allowed for an examination of our water source and showed the potential interaction of species and ARGs residing in the influent and effluent environment. Both microbial profile structure and co-occurrence network analysis provide integrated understanding regarding the diversity of microorganisms and interactions for future advanced water sanitation treatments.

The Evidential Statistics of Genetic Assembly: Bootstrapping a Reference Sequence

The reference sequences play an essential role in genome assembly, like type specimens in taxonomy. Those references are also samples obtained at some time and location with a specific method. How can we evaluate or discriminate uncertainties of the reference itself and assembly methods? Here we bootstrapped 50 random read data sets from a small circular genome of aEscherichia colibacteriophage, phiX174, and tried to reconstruct the reference with 14 free assembly programs. Nine out of 14 assembly programs were capable of circular genome reconstruction. Unicycler correctly reconstructed the reference for 44 out of 50 data sets, but each reconstructed contig of the failed six data sets had minor defects. The other assembly software could reconstruct the reference with minor defects. The defect regions differed among the assembly programs, and the defect locations were far from randomly distributed in the reference genome. All contigs of Trinity included one, but Minia had two perfect copies other than an imperfect reference copy. The centroid of contigs for assembly programs except Unicycler differed from the reference with 75bases at most. Nonmetric multidimensional scaling (NMDS) plots of the centroids indicated that even the reference sequence was located slightly off from the estimated location of the true reference. We propose that the combination of bootstrapping a reference, making consensus contigs as centroids in an edit distance, and NMDS plotting will provide an evidential statistic way of genetic assembly for non-fragmented base sequences.

Use of habitats by aquatic and terrestrial avifauna in tropical coastal lagoons

Tropical coastal lagoons comprise several habitats, which have great importance for avifauna by providing nesting, roosting or foraging sites. However, various anthropogenic activities have caused coastal habitat degradation globally. To sustain conservation, it is crucial to understand the seasonal habitat utilization patterns of avifauna. Additionally, how coastal habitats are influencing terrestrial avifaunal distribution is not well documented. Therefore, this study was carried out to examine the habitat utilization patterns by aquatic and terrestrial avifauna in Batticaloa Lagoon in eastern Sri Lanka from September 2017–August 2018. Compared with past studies, our study indicated a lower diversity of aquatic birds. Findings revealed that 47% and 27% of aquatic and terrestrial avifaunal species, respectively occurred in all habitats indicating their utilization of different habitats as alternative habitats. However, terrestrial bird composition was more similar between the different habitats (compared with aquatic birds) as per non-metric multi-dimensional scaling (NMDS) plots. Overall bird density variation was significant with season and habitat. Considering the avifaunal density, both aquatic and terrestrial birds mostly preferred swamp habitat. Abandoned shrimp farms were least preferred by aquatic birds and terrestrial birds indicating that anthropogenic habitats do not provide many of the required resources that are provided by natural habitats. Mangroves (comprising true mangrove species and mangrove associates) support a relatively high diversity of terrestrial birds, but recorded the lowest diversity of aquatic birds. Suggestions were made to improve habitats to attract more species especially aquatic birds.

Insights into the removal of pharmaceutically active compounds from sewage sludge by two-stage mesophilic anaerobic digestion

The removal efficiencies (REs) of twenty-seven pharmaceutically active compounds (PhACs) (eight analgesic/anti-inflammatories, six antibiotics, four β-blockers, two antihypertensives/diuretics, three lipid regulators and four psychiatric drugs) were evaluated in a pilot-scale two-stage mesophilic anaerobic digestion (MAD) system treating thickened sewage sludge from a pilot-scale A2O™ wastewater treatment plant (WWTP) which was fed with wastewater from the pre-treatment of the full-scale WWTP Murcia Este (Murcia, Spain). The MAD system was long-term operated using two different sets of sludge retention times (SRTs) for the acidogenic (AcD) and methanogenic (MD) digesters (phase I, 2 and 12 days; and phase II, 5 and 24 days, in AcD and MD, respectively). Quantitative PCR (qPCR) and Illumina MiSeq sequencing were used to estimate the absolute abundance of Bacteria, Archaea, and Fungi and investigate the structure, diversity and population dynamics of their communities in the AcD and MD effluents. The extension of the SRT from 12 (phase I) to 24 days (phase II) in the MD was significantly linked with an improved removal of carbamazepine, clarithromycin, codeine, gemfibrozil, ibuprofen, lorazepam, and propranolol. The absolute abundances of total Bacteria and Archaea were higher in the MD regardless of the phase, while the diversity of bacterial and archaeal communities was lower in phase II, in both digesters. Non-metric multidimensional scaling (MDS) plots showed strong negative correlations among phyla Proteobacteria and Firmicutes and between genera Methanosaeta and Methanosarcina throughout the full experimental period. Strong positive correlations were revealed between the relative abundances of Methanospirillum and Methanoculleus and the methanogenesis performance parameters (volatile solids removal, CH4 recovery rate and %CH4 in the biogas), which were also related to longer SRT. The REs of several PhACs (naproxen, ketoprofen, ofloxacin, fenofibrate, trimethoprim, and atenolol) correlated positively (r > 0.75) with the relative abundances of specific bacterial and archaeal groups, suggesting their participation in biodegradation/biotransformation pathways.

TaxonTableTools - A comprehensive, platform-independent graphical user interface software to explore and visualise DNA metabarcoding data

DNA-based identification methods, such as DNA metabarcoding, are increasingly used as biodiversity assessment tools in research and environmental management. Although powerful analysis software exists to process raw data, the translation of sequence read data into biological information and downstream analyses may be difficult for end users with limited expertise in bioinformatics. Thus, the need for easy-to-use, graphical user interface (GUI) software to analyze and visualize DNA metabarcoding data is growing. Here we present TaxonTableTools (TTT), a new platform-independent GUI that aims to fill this gap by providing simple, reproducible analysis and visualization workflows. The input format of TTT is a so-called "TaXon table". This data format can easily be generated within TTT from two common file formats that can be obtained using various published DNA metabarcoding pipelines: a read table and a taxonomy table. TTT offers a wide range of processing, filtering and analysis modules. The user can analyze and visualize basic statistics, such as read proportion per taxon, as well as more sophisticated visualizations such as interactive Krona charts for taxonomic data exploration, or complex parallel category diagrams to assess species distribution patterns. Venn diagrams can be calculated to compare taxon overlap among replicates, samples, or analysis methods. Various ecological analyses can be produced directly, including alpha or beta diversity estimates, rarefaction analyses, and principal coordinate or non-metric multidimensional scaling plots. The taxonomy of a data set can be validated via the Global Biodiversity Information Facility (GBIF) API to check for synonyms and spelling mistakes. Furthermore, geographical distribution data can be automatically downloaded from GBIF. Additionally, TTT offers a conversion tool for DNA metabarcoding data into formats required for traditional, taxonomy-based analyses performed by regulatory bioassessment programs. Beyond that, TTT is able to produce fully interactive html-based graphics that can be analyzed in any web browser. The software comes with a manual and tutorial, is free and publicly available through GitHub (https://github.com/TillMacher/TaxonTableTools) or the Python package index (https://pypi.org/project/taxontabletools/).