Relative Abundance Of Families Research Articles

Physicochemical Variation of Water, Diversity, and Bacterial Community Structure in Post-coal Mining Ponds of Different Ages in Samarinda, East Kalimantan, Indonesia

<p>This study aims to determine physicochemical variation of water, diversity, and community structure of bacteria at post-coal mining ponds of various ages located in Samarinda, East Kalimantan, Indonesia. Bacteria species were identified using a metagenomic approach on the Next-Generation Sequencing (NGS) nanopore platform and analyzed using the QIIME2 pipeline. The result showed that ponds aged > 20 years old had better water quality compared to others < 5 years old. In addition, ponds > 20 years old had lower conductivity values (0,21-0,40 mS/cm), water temperature (29,1-30,1oC), and sulfur content (2,35-6,44 mg/L), as well as higher pH (6,57-7,61) and abundance of sulfur-oxidizing bacteria (SOB) (217-364 CFU/mL). Based on the results, ponds < 5 years old had water quality characterized by higher conductivity (0,27-1,29 mS/cm), water temperature (30,1-31,4 oC), and sulfur content (6,56-15,03 mg/L), lower pH (2,93-3,72), and abundance of SOB (0-38 CFU/mL). Diversity and structure of bacteria community showed that the Operational Taxonomic Unit (OTU) in post-coal mining ponds > 20 years old was 3819 compared to 2027 in those < 5 years old. Bacteria community in post-coal mining ponds > 20 years old consisted of 11 phyla and 45 classes, while those < 5 years old had 9 phyla and 38 classes. Moreover, the relative abundance of families, genera, and species at ponds > 20 years old was also higher. The high water quality, diversity, and community structure of bacteria at ponds > 20 years old showed the successful remediation of ponds water by SOB.</p>

No evidence for temporally balanced selection on larval Pacific oysters Crassostrea gigas: a comment on Durland et al. (2021).

No evidence for temporally balanced selection on larval Pacific oysters Crassostrea gigas: a comment on Durland et al. (2021).

Oregano essential oil improves piglet health and performance through maternal feeding and is associated with changes in the gut microbiota

BackgroundWith a growing demand for safe and sustainable alternatives to antimicrobials, functional feed ingredients such as plant essential oils have been evaluated for their potential to improve gut health. Amongst these, oregano essential oil (OEO) with the main active compounds carvacrol and thymol has been reported to have antimicrobial and antioxidative properties resulting in improved intestinal barrier function and growth in pigs and poultry. However, its impact on the gut microbiota still remains unclear. The aim of this study was to examine the effect of an oregano essential oil phytobiotic on sow and piglet performance and faecal microbiota.ResultsPiglets from OEO supplemented sows were significantly heavier at one week of age and showed a trend for improved average daily weight gain from birth to weaning. Post-weaning, maternally supplemented piglets were numerically heavier at 10 weeks post-weaning and at slaughter with a reduced variability in bodyweight. Health records showed that piglets in the OEO supplemented litters had significantly reduced incidence of therapeutic treatment and reduced mortality. In both sows and piglets, the structure and composition of the faecal microbiota varied considerably over time. Sows supplemented with OEO during lactation showed an increase in the relative abundance of Lactobacillaceae family. In addition, there was an increase in the relative abundance of families known to be important in fibre digestion (Fibrobacteriaceae and Akkermansiaceae). Analysis of piglet microbiota at two weeks and four weeks of age revealed a relative decrease in Enterobacteriaceae while butyrate producers (Lachnospiraceae family) were increased at both timepoints.ConclusionWe hypothesise that the effects observed from this study were exerted through modulation of the gut microbial communities in the sow and her offspring through maternal microbial transfer. Understanding the link between the gut microbiota and dietary factors represents a keystone to improving health and performance for sustainable pig production. Reducing antimicrobial usage can help to reduce the risk of antimicrobial resistance (AMR) which is a global focus for animal production.

Responses of bacterial communities in wheat rhizospheres in different soils to di-n-butyl and di(2-ethylhexyl)phthalate contamination

Di-n-butyl phthalate (DBP) and di(2-ethylhexyl)phthalate (DEHP) are commonly used as plasticizers to enhance the flexibility of plastic products. They are universal pollutants and well-known endocrine disruptors, and their effects on rhizosphere organisms have aroused great concern. In the present study, the effects of DBP and DEHP contamination on bacterial community structure and functions in wheat rhizospheres in fluvo-aquic, cinnamon, and brown soils were investigated using Illumina HiSeq 2500 sequencing. Operational taxonomic unit richness and bacterial diversity were decreased in DEHP-contaminated fluvo-aquic and brown soils, but not in DEHP-contaminated cinnamon and DBP-polluted soils. The relative abundance of some families was positively associated with soil pH, total nitrogen content (TN), and soil organic matter (SOM), and negatively correlated with DBP/DEHP concentration. The relative abundances of families that can extremely effectively degrade DBP/DEHP were enhanced by DBP/DEHP pollution, whereas the relative abundances of some genera that are beneficial to soil health were reduced in the DBP/DEHP-polluted soils. Soil pH, TN, and SOM were crucial in determining the fate and effect of PAEs in the soil ecosystems. In conclusion, DBP/DEHP pollution alters the rhizosphere bacterial community structure and affects microbial metabolic behavior and functional diversity during wheat growth.

Microbiome of a revegetated iron-mining site and pristine ecosystems from the Brazilian Cerrado

The Cerrado domain is composed of different phytophysiognomies and considered a hot spot of global diversity. However, few studies have assessed the soil microbiome of this domain using metabarcoding approach. This study aimed to determine the soil microbiome in a mining site under revegetation and compare with communities of pristine ecosystems. Soil samples were collected in the dry and rainy seasons in an iron-mining site under revegetation (RA), semi-decidual forest (FL), canga (NG) and Cerrado stricto sensu (CE). Soil community was accessed by the amplification of the 16S and 18S ribosomal gene fragments using high-throughput sequencing. The prokaryotic operational taxonomic units (OTUs) were assigned to 18 phyla, 48 classes, 73 orders, 123 families and 168 genera. Acidobacteria and Proteobacteria were the most abundant phylum for FL, CE and RA while Actinobacteria and Acidobacteria were dominant in NG. Relative abundance of families within each phylum varied mainly among sites, but not seasons. For Eukarya, OTUs were assigned to 15 phyla, 35 classes, 94 orders, 168 families and 247 genera. Opisthokonta, SAR (Stramenopiles, Alveolates, and Rhizaria), and Archaeplastida were the most abundant groups for all phytophysiognomies and Fungi accounted for 51–71% of total sequences. Principal coordinate analysis indicates that soil community composition was not influenced by season within each site. We concluded that soil microbiome was dissimilar among sites at the family and genus level but sites shared the same dominant phyla, and that differentiation of soil microbiome was driven mainly by plant community composition.

Towards a competitive solid state fermentation: Cellulases production from coffee husk by sequential batch operation and role of microbial diversity

The cost of cellulases is the main bottleneck for bioethanol production at commercial scale. Solid-state fermentation (SSF) is a promising technology that can potentially reduce cellulases cost by using wastes as substrates. In this work, a SSF system of 4.5L bioreactors was operated continuously by sequential batch operation using the fermented solids from one batch to inoculate the following batch. Coffee husk was used as lignocellulosic substrate. Compost was used as starter in the first batch to provide a rich microbiota. Two strategies were applied: using 10% fermented solids as inoculum in 48h batches (SB90) and using 50% solids in 24h batches (SB50). A consistent and robust production process was achieved by sequential batch operation. Similar cellulase activities around 10 Filter Paper Units per gram of dry solids were obtained through both strategies. Microbial diversity in the starting materials and in the final fermented solids was characterized by next generation sequencing. Microbial composition of both fermented solids was similar but the relative abundance of families and species was affected by the operation strategy used. Main bacteria in the final solids came from compost (families Sphingobacteriaceae, Paenibacillaceae and Xanthomonadaceae), while main fungi families came from coffee husk (families Phaffomycetaceae, Dipodascaceae and two unidentified families of the class of Tramellomycetes). There was a high presence of non-identified mycobiota in the fermented solids. Main identified species were the bacteria Pseudoxanthonomas taiwanensis (12.3% in SB50 and 6.1% in SB90) and Sphingobacterium composti (6.1% in SB50 and 2.6% in SB90) and the yeasts Cyberlindnera jardinii and Barnettozyma californica (17.8 and 4.1% respectively in SB50 and 34 and 9.1% in SB90), all four previously described as lignocellulose degraders. The development of these operational strategies and further biological characterization of the end product could eventually benefit the process economics by providing a standard and specialized inoculum for a continuous SSF for cellulases production.

The longitudinal effect of a multi-strain probiotic on the intestinal bacterial microbiota of neonatal foals.

The microbiota plays a key role in health and disease. Probiotics are a potential way to therapeutically modify the intestinal microbiota and prevent disease. The aim of this study was to investigate the effects of probiotics on the bacterial microbiota of foals during and after administration. Randomised placebo controlled field trial. Thirty-eight healthy neonatal foals enrolled in a previous study were selected. The foals had received a multi-strain probiotic (four Lactobacillus spp. 3-4 × 103 colony-forming units (cfu)/g each, Bifidobacterium animalis spp. lactis, 1 × 103-4 cfu/g) or placebo once daily for 3 weeks. A total of 3 faecal samples were collected from each foal at 2-week intervals and assessed via metagenomic sequencing. The Wilcoxon test was used to compare data between treatment groups. There were no changes on the phylum, order or class level between treatment groups at any age (all P>0.05) but some significant changes in relative abundance of families. Probiotic administration did not result in an increased relative abundance of lactobacilli or bifidobacteria at any age (Lactobacillus: P = 0.9, P = 0.1 and P = 0.2, Bifidobacterium: P = 0.3, P = 0.6 and P = 0.1 for Weeks 2, 4 and 6, respectively). Lactobacillus was enriched in the probiotic group at Week 6 on LEfSe analysis (linear discriminant analysis score 0.34, P = 0 .02). There was no effect on alpha diversity (all P>0.2) or community structure when parsimony and unifrac analysis were applied (all P>0.6). There were limited effects of probiotic treatment on the bacterial microbiota of foals. The studied probiotic based on lactobacilli and bifidobacteria has a limited potential for therapeutic modification of the gastrointestinal microbiota.

Effect of mesohabitats on responses of invertebrate community structure in streams under different land uses.

Riparian vegetation is one of the most important abiotic components determining the water flow pattern in lotic ecosystems, influencing the composition, richness, and diversity of invertebrates. We have identified whether differences in the structure of the assemblages of invertebrates between riffles and pools may influence the responses of fauna to the effects of land use. In addition, we investigated which fauna metrics are responsible for the differentiation between riffles and pools in streams subject to different land uses. During the dry season of 2012, the main substrates of riffles and pools were sampled (Surber collector) from nine streams within forest, pasture, and urban areas. Principal component analysis (PCA) and Permanova showed differences in the set of environmental variables between streams and mesohabitats. The first PCA axis distinguished the forest and pasture streams from the urban area streams and was related to variables indicative of nutrient enrichment and land use, while the second axis was formed by velocity flow and by the quantities of ultrafine and coarse sand, which distinguished the riffles and pools of the streams. The faunal composition distinguished the streams in pasture and forest areas from the urban streams. Riffles and pools were not concordant in the representation of the invertebrate fauna, indicating the importance of sampling both mesohabitats in the types of streams investigated. The richness, taxonomic composition, and relative abundance of families of Ephemeroptera, Plecoptera, and Trichoptera showed robust responses in riffles to the effects of environmental changes, while in pools, only the richness showed a significant response. It was possibly concluded that riffles were more sensitive in detecting the effects of land use. The information from this study help to understand how the community of invertebrates and the types of habitats in streams may be affected by anthropogenic impacts.

Composition, structural characteristics and temporal patterns of fish assemblages in non-tidal Mediterranean lagoons: A case study

The importance of transitional water ecosystems as nursery habitats and feeding grounds for fish species is well-known. Detailed studies of colonization patterns of fish guilds in response to biotic and abiotic drivers are however unevenly distributed among ecosystem types. We address here the temporal variability of fish assemblages in small non-tidal lagoons in the Mediterranean basin. The study was carried out at the Acquatina lagoon (Lecce, Italy) where four stations, situated in two habitat types along a confinement gradient, were sampled twice per month for one year with fyke nets. Forty-five taxa ranging across 20 families were collected, with the most abundant species, Atherina boyeri, accounting for more than 95% of total abundance. Pooling all species together (excluding sand smelt), the structural features of the assemblage, relative abundance of families, and abundance of individual species all showed significant temporal patterns. Mean abundance peaked in Summer and Autumn and fell in Winter, whereas taxonomic richness and diversity were highest in Summer and lowest in Spring. Within the fish assemblage, multivariate ordination showed temporal segregation of species belonging to the same family or genus and expected to be functionally similar, suggesting that they avoid competition for space and resources by timing inward migration and peak occurrence differently. Of the environmental driving forces, which also showed temporal patterns of variation, salinity was the main factor affecting the distribution of individuals and species. The catch of young individuals of several marine species confirmed the role of this small lagoon as a nursery and feeding area, and emphasized the need for further studies.

The diversity of 15 ha of lowland mixed dipterocarp forest, Central Kalimantan

Fifteen hectares of primary forest in Central Kalimantan were enumerated and all trees ≥10 cm dbh tagged and identified to species as far as possible. Tree density, relative abundance of families and species diversity were calculated, as was a mean additive species/area curve for 1 ha and a species/area curve for all 15 ha. The Jaccard index of similarity was also calculated for the 15 plots. The 15 ha enumerated contain 8771 trees with a dbh of ≥10 cm, belonging to 1298 ‘morphospecies’ in 56 families. On average a single plot had 583 trees and 205 species. These figures are within the upper range of species diversity for the Malesian region as a whole. Dipterocarpaceae make up 14% of all trees in the plots, closely followed by Euphorbiaceae with 13%. A surprisingly low coefficient of similarity is found between the plots, the lowest being 3% and the highest 30%. Species/area curve construction showed that the asymptote is not reached in any of the 1 ha plots or when the 15 plots are added together.

Fishbone from the Emily Bay settlement site, Norfolk Island

Fishbone from the settlement site at Emily Bay and excavations in West Emily Bay was identified on the basis of five mouth parts, checked against eight paired bones and some multiple and unique bones. The number of specimens (NISP) was counted and the Minimum Number of Individuals (MNI) calculated to display relative abundance of families. Lethrinidae dominate all assemblages, with Carangidae, Labridae and Serranidae as significant secondaries. Many specimens are large examples of the species. The domination of benthic feeders implies baited hooks, used over submerged reefs close to shore, were probably the most common technology. There are no deep water species present. Norfolk Island fishing appears to be very like that of prehistoric New Zealand.

The generalist pollination system and reproductive success of Calluna vulgaris in the Upper Ardenne

Although specialist pollination systems are often thought to be the outcome of selection, wide evidence exists for generalization within plant-pollinator interactions. We studied the pollination system and reproductive success of Calluna vulgaris (L.) Hull over 3 years in an Upper Ardennes site in Belgium. A wide variety of insect visitors was recorded including Hymenoptera, Diptera, and Lepidoptera. Relative abundance of families and species of visitors varied markedly among years except for bees. Bumblebees and honeybees were the most efficient pollinators at the study site. Syrphid flies, mainly large ones, acted as important co-pollinators because of their high relative frequency. Calluna pollen was also dispersed by wind, and insect-exclusion experiments demonstrated that wind pollination contributed to reproductive success. Following open pollination, fruit set was high, ranging from 82.0 to 97.2% and independent of sampling location. Mean seed number per fruit was less than maximum potential seed number and varied strongly among sampling locations. We discuss this pollination system (generalist insect and wind) in terms of the ecological and geographical success of the species.Key words: Calluna vulgaris, pollinator visitation, insects, wind pollination, reproductive success.

Populations of Arboreal Spiders (Araneae) on Douglas-Firs and True Firs in the Interior Pacific Northwest

Population densities and relative abundances of spider families were estimated on Douglas-fir, Pseudotsugata menziessii var. glauca (Beissn.) Franco and true firs, Abies spp., in three geographical provinces of the interior Pacific Northwest: the Southern Cascades, the Northern Cascades, and the Blue Mountains. Mean densities, estimated by sampling tree foliage on lower branches in June 1981, were 9.96, 5.21, and 6.03 spiders per square meter of branch area for the three areas, respectively. Eleven families were represented in the sample. Over half of all individuals were hunting spiders of the families Salticidae and Philodromidae, of which several species are believed to be important predators of defoliating insects. The rest were web-spinners, mostly of the families Dictynidae, Araneidae, Linyphiidae, and Theridiidae. The relative abundance of families had a consistent statistical pattern in which their frequencies were apportioned according to a log series distribution. This suggests that arboreal spider communities of interior Pacific Northwest fir stands have a similar familial structure, probably determined by the branch and foliage characteristics of their habitat.