Mixed effects of climate and species richness on aboveground carbon stock in subtropical Atlantic forests

Tropical forests are global biodiversity hotspots and are crucial in the global carbon (C) cycle. Understanding the drivers of aboveground carbon stock (AGC) in a heterogeneous and biodiverse system can shed light on the processes underlying the relationship between biodiversity and carbon accumulation. Here, we investigate how biodiversity, environment, and landscape structure affect AGC. We examined such associations in 349 plots comprising over 95,346 km2 the Atlantic Forest of southern Brazil, encompassing three forest types: Dense Ombrophylous Forest (DF), Mixed Ombrophylous Forest (MF), and Seasonal Deciduous Forest (SF). Each plot was described by environmental variables, landscape metrics, and biodiversity (species richness and functional diversity). We used diversity, environmental, and landscape variables to build generalized linear mixed models and understand which can affect the forest AGC. We found that species richness is associated positively with AGC in all forest types, combined and separately. Seasonal temperature and isothermality affect AGC in all forest types; additionally, stocks are positively influenced by annual precipitation in SF and isothermality in MF. Among landscape metrics, total fragment edge negatively affects carbon stocks in MF. Our results show the importance of species diversity for carbon stocks in subtropical forests. The climate effect was also relevant, showing the importance of these factors, especially in a world where climate change tends to affect forest stock capacity negatively.

Dissimilarity of megabenthic community structure between deep-water seamounts with cobalt-rich crusts: Case study in the northwestern Pacific Ocean

As anthropogenic disturbance on deep-sea seamount ecosystems grows, there is an urgent need for a better understanding of the biodiversity and community structure in benthic ecosystems, which can vary at local and regional scales. A survey of the benthic megafauna on two adjacent deep-water seamounts in the northwestern Pacific Ocean was conducted, which are covered by cobalt-rich crusts, to assess the biodiversity patterns and dissimilarity of assemblage composition. Based on a multidisciplinary dataset generated from video recordings, multibeam bathymetry data, and near-bottom currents, environmental and spatial factors impacting the megabenthic communities were explored. Results showed that these two deep-water seamounts were dominated by hexactinellids, crinoids, and octocorals. The seamounts were able to support diverse and moderately abundant megafauna, with a total of 6436 individuals classified into 94 morphospecies. The survey covered a distance of 52.2 km across a depth range of 1421-3335 m, revealing multiple distinct megabenthic assemblages. The megabenthic communities of the two deep-water seamounts, with comparable environmental conditions, exhibited similarities in overall density, richness, and faunal lists, while dissimilarities in the relative abundance of taxa and assemblage composition. No gradual depth-related change in terms of abundance, richness, or species turnover was observed across the two seamounts, despite the statistical significance of depth in structuring the overall communities. The spatial distribution of megabenthic communities displayed a discontinuous and patchy pattern throughout the two deep-water seamounts. This patchiness was driven by the interactive effects of multiple environmental factors. Near-bottom currents and microhabitat features were the primary drivers influencing their dissimilarities in megabenthic community structure. This case study on the megabenthic community structure of two adjacent seamounts with cobalt-rich crusts can serve as an environmental baseline, providing a reference status for the conservation and management of seamount ecosystems, particularly valuable for areas being considered for deep-sea mining.

Stochastic process drives the dissimilarity in biodiversity patterns between Pinus kwangtungensis coniferous forest and evergreen deciduous broad-leaved mixed forest in karst area

Pinus kwangtungensis is an endangered evergreen conifer tree species, and its in situ conservation has been considered one of the most critical issues. However, relative protection is limited by the lack of understanding of its community structure and underlying assembly processes. To study how the species diversity and assembly processes of Pinus kwangtungensis coniferous forest (CF) differed with regional climax community, this study established a series forest dynamic plots both in CF and evergreen deciduous broadleaved mixed forest (EDBM). By performing comparison analysis and PER-SIMPER approaches, we quantified the differences in species diversity and community assembly rules. The results showed that the species α-diversity of CF differed greatly from the EDBM both in species richness and evenness. In addition, the stochastic process acted a more important role in determining species composition, indicating the uncertainty in presence of species. The soil phosphorus and changeable calcium content were the main factors driving the differences in biodiversity, which the importance of soil nutrient factors in driving species composition. Our study highlighted that we should consider the community structure and ecological process when conducting conservation of Pinus kwangtungensis.

Microbiota diversity and anti-Pseudogymnoascus destructans bacteria isolated from Myotis pilosus skin during late hibernation

Symbiotic microorganisms that reside on the host skin serve as the primary defense against pathogens in vertebrates. Specifically, the skin microbiome of bats may play a crucial role in providing resistance against Pseudogymnoascus destructans (Pd), the pathogen causing white-nose syndrome. However, the epidermis symbiotic microbiome and its specific role in resisting Pd in highly resistant bats in Asia are still not well understood. In this study, we collected and characterized skin microbiota samples of 19 Myotis pilosus in China and explored the differences between Pd-positive and negative individuals. We identified inhibitory effects of these bacteria through cultivation methods. Our results revealed that the Simpson diversity index of the skin microbiota for positive individuals was significantly lower than that of negative individuals, and the relative abundance of Pseudomonas was significantly higher in positive bats. Regardless of whether individuals were positive or negative for Pd, the relative abundance of potentially antifungal genera in skin microbiota was high. Moreover, we successfully isolated 165 microbes from bat skin and 41 isolates from positive individuals able to inhibit Pd growth compared to only 12 isolates from negative individuals. A total of 10 genera of Pd-inhibiting bacteria were screened, among which the genera Algoriella, Glutamicibacter, and Psychrobacter were newly discovered as Pd-inhibiting genera. These Pd-inhibiting bacteria metabolized a variety of volatile compounds, including dimethyl trisulfide, dimethyl disulfide, propylene sulfide, 2-undecanone, and 2-nonanone, which were able to completely inhibit Pd growth at low concentrations.IMPORTANCERecently, white-nose syndrome has caused the deaths of millions of hibernating bats, even threatening some with regional extinction. Bats in China with high resistance to Pseudogymnoascus destructans can provide a powerful reference for studying the management of white-nose syndrome and understanding the bats against the pathogen's intrinsic mechanisms. This study sheds light on the crucial role of host symbiotic skin microorganisms in resistance to pathogenic fungi and highlights the potential for harnessing natural defense mechanisms for the prevention and treatment of white-nose syndrome. In addition, this may also provide promising candidates for the development of bioinsecticides and fungicides that offer new avenues for addressing fungal diseases in wildlife and agricultural environments.

A century of statistical Ecology

As data and computing power have surged in recent decades, statistical modeling has become an important tool for understanding ecological patterns and processes. Statistical modeling in ecology faces two major challenges. First, ecological data may not conform to traditional methods, and second, professional ecologists often do not receive extensive statistical training. In response to these challenges, the journal Ecology has published many innovative statistical ecology papers that introduced novel modeling methods and provided accessible guides to statistical best practices. In this paper, we reflect on Ecology's history and its role in the emergence of the subdiscipline of statistical ecology, which we define as the study of ecological systems using mathematical equations, probability, and empirical data. We showcase 36 influential statistical ecology papers that have been published in Ecology over the last century and, in so doing, comment on the evolution of the field. As data and computing power continue to increase, we anticipate continued growth in statistical ecology to tackle complex analyses and an expanding role for Ecology to publish innovative and influential papers, advancing the discipline and guiding practicing ecologists.

The Fungal Diversity and Potential Pathogens Associated with Postharvest Fruit Rot of 'Huangguan' Pear (Pyrus bretschneideri) in Hebei Province, China

Postharvest fruit rot caused by pathogens is a serious problem in the pear industry. This study investigated the fungal diversity and main pathogens and identified a new pathogen in the stored 'Huangguan' pear (Pyrus bretschneideri Rehd.), the dominant pear variety in northern China. We sampled 20 refrigeration houses from five main producing regions in Hebei Province and used Illumina sequencing technology to detect the fungal composition. Alternaria (56.3%) was the most abundant fungus, followed by Penicillium (9.2%) and Monilinia (6.2%). We also isolated and identified nine strains of Alternaria and four strains of Penicillium. Moreover, we observed a new postharvest fruit disease in 'Huangguan' pear caused by Stemphylium eturmiunum, which was confirmed by phylogenetic analysis by combining the sequences of three conserved genes, including internal transcribed spacer, gapdh, and calmodulin. This study marks the first documentation of S. eturmiunum causing fruit rot in 'Huangguan' pears, offering valuable insights for identifying and controlling this newly identified postharvest disease.

Geographical association of biodiversity with cancer and cardiovascular mortality rates: analysis of 39 distinct conditions

Background

Biodiversity has been recognized as a positive contributor to human health and wellbeing. Cardiovascular disease and cancer are the two most significant global health burdens, and understanding their relationship with biodiversity forms an essential step toward promoting biodiversity conservation and human health.

Methods

The species richness of birds is a common indicator of biodiversity, given their vast numbers, distinctive distribution, and acute sensitivity to environmental disturbances. This ecological study utilized avian observation data derived from the eBird database, human health data from the International Health Metrics and Evaluation, and county-level statistics, including population characteristics, socio-economics, healthcare service, residential environment, and geographic and climatic characteristics in 2014. We aimed to extensively explore the individual associations between biodiversity (i.e., avian species richness) and age-standardized cause-specific mortalities for different types of cancers (29 conditions) and cardiovascular diseases (10 conditions) across the United States (US).

Results

Our multiple regression analyses that adjusted for a variety of socio-demographic and geographical factors showed that increased rarefied species richness of birds was associated with reduced mortality rates for three of the five most common cancers, namely, tracheal, bronchus, and lung cancer, breast cancer (in women only), and colon and rectal cancer. For cardiovascular conditions, a similar relationship was observed for ischemic heart disease and cerebrovascular disease-the two most frequent causes of mortality. This study provided extended details regarding the beneficial effects of biodiversity on human health.

Analysis and Functional Prediction of Core Bacteria in the Arabidopsis Rhizosphere Microbiome under Drought Stress

The effects of global warming, population growth, and economic development are increasing the frequency of extreme weather events, such as drought. Among abiotic stresses, drought has the greatest impact on soil biological activity and crop yields. The rhizosphere microbiota, which represents a second gene pool for plants, may help alleviate the effects of drought on crops. In order to investigate the structure and diversity of the bacterial communities on drought stress, this study analyzed the differences in the bacterial communities by high-throughput sequencing and bioinformatical analyses in the rhizosphere of Arabidopsis thaliana under normal and drought conditions. Based on analysis of α and β diversity, the results showed that drought stress had no significant effect on species diversity between groups, but affected species composition. Difference analysis of the treatments showed that the bacteria with positive responses to drought stress were Burkholderia-Caballeronia-Paraburkholderia (BCP) and Streptomyces. Drought stress reduced the complexity of the rhizosphere bacterial co-occurrence network. Streptomyces was at the core of the network in both the control and drought treatments, whereas the enrichment of BCP under drought conditions was likely due to a decrease in competitors. Functional prediction showed that the core bacteria metabolized a wide range of carbohydrates, such as pentose, glycans, and aromatic compounds. Our results provide a scientific and theoretical basis for the use of rhizosphere microbial communities to alleviate plant drought stress and the further exploration of rhizosphere microbial interactions under drought stress.

Foodborne Pathogen and Microbial Community Differences in Fresh Processing Tomatoes in Xinjiang, China

The microbes on fresh processing tomatoes correlate closely with diseases, preservation, and quality control. Investigation of the microbial communities on processing tomatoes from different production regions may help define microbial specificity, inform disease prevention methods, and improve quality. In this study, surface microbes on processing tomatoes from 10 samples in two primary production areas of southern and northern Xinjiang were investigated by sequencing fungal internal transcribed spacer and bacterial 16S rRNA hypervariable sequences. A total of 133 different fungal and bacterial taxonomies were obtained from processing tomatoes in the two regions, of which 63 genera were predominant. Bacterial and fungal communities differed significantly between southern and northern Xinjiang, and fungal diversity was higher in southern Xinjiang. Alternaria and Cladosporium on processing tomatoes in southern Xinjiang were associated with plant pathogenic risk. The plant pathogenic fungi of processing tomatoes in northern Xinjiang were more abundant in Alternaria and Fusarium. The abundance of Alternaria on processing tomatoes was higher in four regions of northern Xinjiang, indicating that there is a greater risk of plant pathogenicity in these areas. Processing tomatoes in northern and southern Xinjiang contained bacterial genera identified as gut microbes, such as Pantoea, Erwinia, Enterobacter, Enterococcus, and Serratia, indicating the potential risk of contamination of processing tomatoes with foodborne pathogens. This study highlighted the microbial specificity of processing tomatoes in two tomato production regions, providing a basis for further investigation and screening for foodborne pathogenic microorganisms.

Temporal patterns of bacterial communities in the Billings Reservoir system

In this study, high-throughput sequencing of 16S rRNA amplicons and predictive PICRUSt functional profiles were used to perform a comprehensive analysis of the temporal bacterial distribution and metabolic functions of 19 bimonthly samples collected from July 2019 to January 2020 in the surface water of Billings Reservoir, São Paulo. The results revealed that most of the bacterial 16S rRNA gene sequences belonged to Cyanobacteria and Proteobacteria, which accounted for more than 58% of the total bacterial abundance. Species richness and evenness indices were highest in surface water from summer samples (January 2020), followed by winter (July 2019) and spring samples (September and November 2019). Results also showed that the highest concentrations of sulfate (SO4-2), phosphate (P), ammonia (NH3), and nitrate (NO3-) were detected in November 2019 and January 2020 compared with samples collected in July and September 2019 (P < 0.05). Principal component analysis suggests that physicochemical factors such as pH, DO, temperature, and NH3 are the most important environmental factors influencing spatial and temporal variations in the community structure of bacterioplankton. At the genus level, 18.3% and 9.9% of OTUs in the July and September 2019 samples, respectively, were assigned to Planktothrix, while 14.4% and 20% of OTUs in the November 2019 and January 2020 samples, respectively, were assigned to Microcystis. In addition, PICRUSt metabolic analysis revealed increasing enrichment of genes in surface water associated with multiple metabolic processes rather than a single regulatory mechanism. This is the first study to examine the temporal dynamics of bacterioplankton and its function in Billings Reservoir during the winter, spring, and summer seasons. The study provides comprehensive reference information on the effects of an artificial habitat on the bacterioplankton community that can be used to interpret the results of studies to evaluate and set appropriate treatment targets.

Effects of Weight Gain During Pregnancy in Normal-Weight Women on Changes in the Gut Microbiota of Pregnant Women in the Third Trimester

With the improvement of living standards and the lack of nutrition awareness during pregnancy, the phenomenon of excessive weight gain (EWG) of pregnancy is increasing. EWG during pregnancy has profound effects on the health of mother and offspring. The role of intestinal flora in regulating metabolic diseases has gradually attracted attention in recent years. The study explored the effect of EWG during pregnancy on gut microbiota, and analyzed the diversity and composition of gut microbiota in pregnant women in third trimester. Fecal samples were collected and divided into: insufficient weight gain (IWG) during pregnancy (group A1, N = 4), and appropriate weight gain (AWG) during pregnancy (group A2, N = 9), and EWG during pregnancy (N = 9 in A3 group). MiSeq high-throughput sequencing technology and bioinformatics analysis were introduced to investigate relationship of gestational weight gain and maternal gut microbiota. General data analysis showed that gestational weight gain and delivery mode have significant differences among the three groups. The overall level and diversity of intestinal microbiota in A1 and A3 group were increased. Composition of gut microbiota has no difference among three groups at the phylum level, but species of gut microbiota were different. Alpha diversity index analysis showed that the richness of A3 group was increased versus A2 group. EWG during pregnancy affects the abundance and proportion of gut microbiota in the third trimester. Therefore, maintaining moderate weight gain during pregnancy helps to maintain intestinal homeostasis.

Gut Microbiota Combined with Serum Metabolomics to Investigate the Hypoglycemic Effect of Actinidia arguta Leaves

Actinidia arguta leaves (AAL) are an excellent source of bioactive components for the food industry and possess many functional properties. However, the hypoglycemic effect and mechanism of AAL remain unclear. The aim of this work was to investigate the potential hypoglycemic effect of AAL and explore its possible mechanism using 16S rRNA sequencing and serum metabolomics in diabetic mice induced by high-fat feeding in combination with streptozotocin injection. A total of 25 flavonoids from AAL were isolated and characterized, and the contents of the extract from the AAL ranged from 0.14 mg/g DW to 8.97 mg/g DW. The compound quercetin (2) had the highest content of 8.97 ± 0.09 mg/g DW, and the compound kaempferol-3-O-(2'-O-D-glucopyl)-β-D-rutinoside (12) had the lowest content of 0.14 ± 0.01 mg/g DW. In vivo experimental studies showed that AAL reduced blood glucose and cholesterol levels, improved insulin sensitivity, and ameliorated oxidative stress and liver and kidney pathological damage. In addition, gut microbiota analysis found that AAL significantly reduced the F/B ratio, enriched the beneficial bacteria Bacteroides and Bifidobacterium, and inhibited the harmful bacteria Lactobacillus and Desulfovibrio, thereby playing an active role in intestinal imbalance. In addition, metabolomics analysis showed that AAL could improve amino acid metabolism and arachidonic acid metabolism, thereby exerting a hypoglycemic effect. This study confirmed that AAL can alleviate type 2 diabetes mellitus (T2DM) by regulating intestinal flora and interfering with related metabolic pathways, providing a scientific basis for its use as a dietary supplement and for further exploration of the mechanism of AAL against T2DM.

Host-bacteriome transplants of the schistosome snail host Biomphalaria glabrata reflect species-specific associations

Microbial symbionts can affect host phenotypes and, thereby, ecosystem functioning. The microbiome is increasingly being recognized as an important player in the tripartite interaction between parasitic flatworms, snail intermediate hosts, and the snail microbiome. In order to better understand these interactions, transplant experiments are needed, which rely on the development of a reliable and reproducible protocol to obtain microbiome-disturbed snails. Here, we report on the first successful snail bacteriome transplants, which indicate that Biomphalaria glabrata can accrue novel bacterial assemblies depending on the available environmental bacteria obtained from donor snails. Moreover, the phylogenetic relatedness of the donor host significantly affected recipients' survival probability, corroborating the phylosymbiosis pattern in freshwater snails. The transplant technique described here, complemented by field-based studies, could facilitate future research endeavors to investigate the role of specific bacteria or bacterial communities in parasitic flatworm resistance of B. glabrata and might ultimately pave the way for microbiome-mediated control of snail-borne diseases.

Relating biodiversity with health disparities of human population: An ecological study across the United States

Understanding biodiversity's contributions to human health is the first step toward fostering synergies between biodiversity conservation and health promotion - two major targets of UN's Sustainable Development Goals. The One Health approach acknowledges the health of people and biodiversity are interconnected and facing common threats. In this study, we aimed to unveil the geographical association between avian biodiversity and population health across the US. In this ecological study, we combined citizen science bird data from eBird, population health data from the Institute for Health Metrics and Evaluation, and county-level statistics of population characteristics, including socio-economics, healthcare service etc. Multivariate linear regression analyses were performed between bird biodiversity (measured by rarefied species richness of birds), key indicators of general public health (e.g., cause-specific mortality rate), and socio-economic health determinants of 2751 US counties. We found that a higher number of bird species was significantly associated with longer life expectancy after confounding adjustment (regression coefficient (95% CIs), 0·005 (0·003, 0·008)). Bird species richness calculated using the rarefied method consistently accounted for variance in age-specific mortality risks in both very young and old age groups (R² from 2% to 4%). Rarefied species richness of birds was negatively correlated with the majority of cause-specific deaths (12 out of 21 mutually exclusive causes of death), indicating a general synergy effect between biodiversity and human health. The associations with the top causes of deaths were regarded as highly significant, with considerable effect sizes, for example, for cardiovascular diseases (regression coefficient (95% CIs), -0·242 (-0·311, -0·174)). Our findings show human health is inseparable from the health of the shared environment and the well-being of all species. Bird species richness offers a valuable means to understand large-scale relationships between human health and the health of the environment. To enable equitable sharing of biodiversity's benefits to human health, more efforts should be made to understand two-way socio-ecological mechanism underlying human-biodiversity interactions.

Monitoring insect biodiversity and comparison of sampling strategies using metabarcoding: A case study in the Yanshan Mountains, China

Insects are the richest and most diverse group of animals and yet there remains a lack, not only of systematic research into their distribution across some key regions of the planet, but of standardized sampling strategies for their study. The Yanshan Mountains, being the boundary range between the Inner Mongolian Plateau and the North China Plain, present an indispensable piece of the insect biodiversity puzzle: both requiring systematic study and offering opportunities for the development of standardized methodologies. This is the first use of DNA metabarcoding to survey the insect biodiversity of the Yanshan Mountains. The study focuses on differences of community composition among samples collected via different methods and from different habitat types. In total, 74 bulk samples were collected from five habitat types (scrubland, woodland, wetland, farmland and grassland) using three collection methods (sweep netting, Malaise traps and light traps). After DNA extraction, PCR amplification, sequencing and diversity analysis were performed, a total of 7427 Operational Taxonomic Units (OTUs) at ≥97% sequence similarity level were delimited, of which 7083 OTUs were identified as belonging to Insecta. Orthoptera, Diptera, Coleoptera and Hemiptera were found to be the dominant orders according to community composition analysis. Nonmetric multidimensional scaling (NMDS) analysis based on Bray-Curtis distances revealed highly divergent estimates of insect community composition among samples differentiated by the collection method (R = .524802, p = .001), but nonsignificant difference among samples differentiated according to habitat (R = .051102, p = .078). The study therefore appears to indicate that the concurrent use of varied collection methods is essential to the accurate monitoring of insect biodiversity.

Species diversity pattern and its drivers of the understory herbaceous plants in a Chinese subtropical forest

Understory herbaceous plants are an important component of forest ecosystems, playing important roles in species diversity and forest dynamics in forests. However, the current understanding of the biodiversity of forest communities is mostly from woody plants, and knowledge of community structure and species diversity for understory herbaceous plants remains scarce. In a subtropical forest in China, we investigated understory vascular herbaceous diversity from 300 plots (5 × 5 m) in the main growing season. In this study, we analyzed the community structure and diversity pattern of the understory herbaceous community and linked the species diversity pattern to both abiotic and biotic environments. We found a rich diversity of understory herbaceous communities in this forest (81 species belonging to 55 genera), and floristic elements at the genus level were dominated by tropical elements, followed by temperate elements. The diversity pattern of the understory herbaceous showed a significant habitat preference, with the highest diversity in the lowland valleys and then followed by in middle slopes. In addition, herbaceous diversity was significantly affected by both abiotic factors (such as terrain convexity) and biotic factors (such as the diversity of surrounding woody plants). Our study indicated that species diversity of understory herbaceous showed a remarkable habitat preference, such as lowland valleys, and highlighted the importance of both abiotic and biotic environments in driving herbaceous diversity patterns in the subtropical forest understory.

Metabarcoding of bacteria and parasites in the gut of Apodemus agrarius

BACKGROUND

The striped field mouse Apodemus agrarius is a wild rodent commonly found in fields in Korea. It is a known carrier of various pathogens. Amplicon-based next-generation sequencing (NGS) targeting the 16S ribosomal RNA (rRNA) gene is the most common technique used to analyze the bacterial microbiome. Although many bacterial microbiome analyses have been attempted using feces of wild animals, only a few studies have used NGS to screen for parasites. This study aimed to rapidly detect bacterial, fungal and parasitic pathogens in the guts of A. agrarius using NGS-based metabarcoding analysis.

METHODS

We conducted 18S/16S rDNA-targeted high-throughput sequencing on cecal samples collected from A. agrarius (n = 48) trapped in May and October 2017. Taxa of protozoa, fungi, helminths and bacteria in the cecal content were then identified.

RESULTS

Among the protozoa identified, the most prevalent was Tritrichomonas sp., found in all of the cecal samples, followed by Monocercomonas sp. (95.8% prevalence; in 46/48 samples) and Giardia sp. (75% prevalence; in 36/48 samples). For helminths, Heligmosomoides sp. was the most common, found in 85.4% (41/48) of samples, followed by Hymenolepis sp. (10.4%; 5/48) and Syphacia sp. (25%; 12/48). The 16S rRNA gene analysis showed that the microbial composition of the cecal samples changed by season (P = 0.005), with the linear discriminant analysis effect size showing that in the spring Escherichia coli and Lactobacillus murinus were more abundant and Helicobacter rodentium was less abundant. Helicobacter japonicus was more abundant and Prevotella_uc was less abundant in males. The microbial composition changed based on the Heligmosomoides sp. infection status (P = 0.019); specifically, Lactobacillus gasseri and Lactobacillus intestinalis were more abundant in the Heligmosomoides sp.-positive group than in the Heligmosomoides sp.-negative group.

CONCLUSIONS

This study demonstrated that bacterial abundance changed based on the season and specific parasitic infection status of the trapped mice. These results highlight the advantages of NGS technology in monitoring zoonotic disease reservoirs.

Root-Zone Restriction Regulates Soil Factors and Bacterial Community Assembly of Grapevine

Root-zone restriction induces physiological stress on roots, thus limiting the vegetative and enhancing reproductive development, which promotes fruit quality and growth. Numerous bacterial-related growth-promoting, stress-mitigating, and disease-prevention activities have been described, but none in root-restricted cultivation. The study aimed to understand the activities of grapevine bacterial communities and plant-bacterial relationships to improve fruit quality. We used High-throughput sequencing, edaphic soil factors, and network analysis to explore the impact of restricted cultivation on the diversity, composition and network structure of bacterial communities of rhizosphere soil, roots, leaves, flowers and berries. The bacterial richness, diversity, and networking were indeed regulated by root-zone restriction at all phenological stages, with a peak at the veraison stage, yielding superior fruit quality compared to control plants. Moreover, it also handled the nutrient availability in treated plants, such as available nitrogen (AN) was 3.5, 5.7 and 0.9 folds scarcer at full bloom, veraison and maturity stages, respectively, compared to control plants. Biochemical indicators of the berry have proved that high-quality berry is yielded in association with the bacteria. Cyanobacteria were most abundant in the phyllosphere, Proteobacteria in the rhizosphere, and Firmicutes and Bacteroidetes in the endosphere. These bacterial phyla were most correlated and influenced by different soil factors in control and treated plants. Our findings are a comprehensive approach to the implications of root-zone restriction on the bacterial microbiota, which will assist in directing a more focused procedure to uncover the precise mechanism, which is still undiscovered.

The temporal and spatial endophytic fungal community of Huperzia serrata: diversity and relevance to huperzine A production by the host

BACKGROUND

Plants maintain the steady-state balance of the mutually beneficial symbiosis relationship with their endophytic fungi through secondary metabolites. Meanwhile endophytic fungi can serve as biological inducers to promote the biosynthesis and accumulation of valuable secondary metabolites in host plants through a variety of ways. The composition and structure of endophytic fungal community are affected by many factors, including tissues, seasons and so on. In this work, we studied the community diversity, temporal and spatial pattern of endophytic fungi detected from the roots, stems and leaves of Huperzia serrata in different seasons. The correlation between endophytic fungi and huperzine A (HupA) content in plants was analyzed.

RESULTS

A total of 7005 operational taxonomic units were detected, and all strains were identified as 14 phyla, 54 classes, 140 orders, 351 families and 742 genera. Alpha diversity analysis showed that the diversity of endophytic fungi in stem and leaf was higher than that in root, and the diversity in summer (August) was lower than that in other months. NMDS analysis showed that the endophytic fungal communities of leaves, stems and roots were significantly different, and the root and leaf communities were also different between four seasons. Through correlation analysis, it was found that 33 genera of the endophytic fungi of H. serrata showed a significant positive correlation with the content of HupA (p < 0.05), of which 13 genera (Strelitziana, Devriesia, Articulospora, Derxomyces, Cyphellophora, Trechispora, Kurtzmanomyces, Capnobotryella, Erythrobasidium, Camptophora, Stagonospora, Lachnum, Golubevia) showed a highly significant positive correlation with the content of HupA (p < 0.01). These endophytic fungi may have the potential to promote the biosynthesis and accumulation of HupA in plant.

CONCLUSIONS

This report is the first time to analyze the diversity of endophytic fungi in tissues of H. serrata in different seasons, which proves that there is variability in different tissues and seasonal distribution patterns. These findings provide references to the study of endophytic fungi of H. serrata.

The microbial communities (bacteria, algae, zooplankton, and fungi) improved biofloc technology including the nitrogen-related material cycle in Litopenaeus vannamei farms

Microbes are essential in biofloc technology for controlling nitrogen levels in water. The composition and function of microorganisms with biofloc systems were reported; however, data on microorganisms other than bacteria, such as algae (which are essential in the nitrogen cycle) and zooplankton (which are bacterial and algal predators), remain limited. The microbial communities (including bacteria, algae, zooplankton, and fungi) were investigated in shrimp farms using biofloc technology. Using Illumina MiSeq sequencing, the V4 region of 18S rRNA and the V3-V4 region of 16S rRNA were utilized for the analysis of the eukaryotic and prokaryotic microbial communities. As a result, it was found that the biofloc in the shrimp farm consisted of 48.73%-73.04% eukaryotic organisms and 26.96%-51.27% prokaryotic organisms. In these shrimp farms, prokaryotic microbial communities had higher specie richness and diversity than eukaryotic microbial communities. However, the eukaryotic microbial communities were more abundant than their prokaryotic counterparts, while algae and zooplankton dominated them. It was discovered that the structures of the microbial communities in the shrimp farms seemed to depend on the effects of predation by zooplankton and other related organisms. The results provided the nitrogen cycle in biofloc systems by the algal and bacterial groups in microbial communities.

Tree diversity in a tropical agricultural-forest mosaic landscape in Honduras

Biodiversity decline in the tropics requires the implementation of comprehensive landscape management where agricultural systems are necessarily an integral element of biodiversity conservation. This study evaluates the potential for taxonomic biodiversity conservation within an intensive livestock-agricultural-forest mosaic landscape in Catacamas, Honduras. Tree sampling was performed in 448 plots set up within different forest and agricultural land uses: secondary forests, agroforestry coffee plantations, agriculture, pastures, live fences and riparian forest. All trees with a minimum diameter at breast height of 10 cm were identified and measured. We characterized their tree structure and diversity, and compared tree diversity between the different uses. The results indicate a high degree of tree species diversity: 375 species identified, belonging to 74 families among the 15,096 trees inventoried across 84.2 hectares, including many rare species (40% of the species registered three individuals or fewer). Biodiversity indices for agroforestry coffee were found equivalent to those for natural secondary forests in the Catacamas landscape. Combining biodiversity conservation and agricultural production is possible in human-pressured tropical landscapes through tree cover maintenance. Enrichment practices combining local producers and technical knowledge may improve tree diversity in agricultural landscapes by prioritizing a mix of forest and introduced tree species (rare and with multiple uses).

Mycotoxin Production and the Relationship between Microbial Diversity and Mycotoxins in Pyrus bretschneideri Rehd cv. Huangguan Pear

Mycotoxins are generated by a series of fungal pathogens in postharvest fruit, resulting in serious health threat to consumers and great economic loss to the fruit storage industry. The microbial differences between rotten and healthy fruit during storage and their relationship with mycotoxin production have not been fully studied. In this study, differences in microbial diversity between rotten and healthy fruit after 30 days of storage at ambient temperature were investigated using high-throughput sequencing technology in 'Huangguan' pear (Pyrus bretschneideri Rehd cv. Huangguan) harvested from five different producing regions of Hebei province, China. The bacterial genus Gluconobacter was much more abundant in rotten fruit (76.24%) than that in healthy fruit (32.36%). In addition, Komagataeibacter and Acetobacter were also relatively higher in abundance in rotten fruit. In contrast, bacterial genera Pantoea, Alistipes, Muribaculaceae, Lactobacillus, and Ruminococcaceae_UCG were found to be more abundant in healthy fruit. Fungal genera including Botryosphaeria, Colletotrichum, Valsa, Alternaria, Rosellinia, Fusarium, and Trichothecium were found to be abundant in rotten fruit. The results of principal coordinate analysis (PCoA) showed that there were significant differences in the microbial diversity of different regions. PAT (patulin) was detected in all rotten fruit samples, while tenuazonic acid (TeA), alternariol (AOH), and alternariolmonomethyl ether (AME) were only detected in samples collected from one region (Weixian). Canonical correlation analysis (CCA) and Pearson correlation analysis showed that the abundance of Alistipes and Pantoea were negatively correlated with the contents of PAT, suggesting that bacterial genera Alistipes and Pantoea have potential in reducing mycotoxin production in 'Huangguan' pear.

Effect of sex on the gut microbiota characteristics of passerine migratory birds

The gut microbiota, considered the “invisible organ” in the host animal, has been extensively studied recently. However, knowledge about the gut microbiota characteristics of passerine migratory birds during migration is limited. This study investigated the gut microbiota characteristics of three dominant migratory bird species (namely orange-flanked bluetail Tarsiger cyanurus, yellow-throated bunting Emberiza elegans, and black-faced bunting Emberiza spodocephala) in the same niche during spring migration and whether they were bird sex-specific. The compositions of gut microbiota species in these three migratory bird species and their male and female individuals were found to be similar. The main bacterial phyla were Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes, and the main genera were Lactobacillus, Acinetobacter, Rickettsiella, and Mycobacterium; however, their relative abundance was different. Moreover, some potential pathogens and beneficial bacteria were found in all the three bird species. Alpha diversity analysis showed that in T. cyanurus, the richness and diversity of the gut microbiota were higher in male individuals than in female individuals, while the opposite was true for E. elegans and E. spodocephala. The alpha diversity analysis showed significant differences between male and female individuals of E. elegans (p < 0.05). The beta diversity analysis also revealed that the gut microbial community structure differed significantly between the male and female individuals of the three migratory bird species.

Correlation between the Concentration of Secondary Metabolites and Soil Microorganisms in Sophora Koreensis Nakai from Different Habitat

Sophora koreensis is an endemic species of Gangwon-do, Korea, that has a variety of applications for foods and for folk remedies. Here this research analyzed and compared compounds present in leaves, stems, and roots of S. koreensis collected from three different habitats in Chuncheon, Inje and Yanggu in South Korea. This research also analyzed soil microorganisms present in the three habitats to determine the correlation between the compound and microorganisms. N-methylcytisine was the most common compound in all three habitats, but the amounts varied with Chuncheon having the highest amount (509 mg/L), followed by Yanggu and Inje(102 mg/L and 39 mg/L, respectively). The composition of microorganisms also varied by habitat. Yanggu, Inje, and Chuncheon had 1013, 973, and 814 taxa, respectively. According to the phylogenetic relations, the composition of the soil microorganisms in Chuncheon was significantly different from the other two. It contained more PAC000121_g (Solibacteres), major taxa in all three habitats (14% in Chuncheon). In contrast less Opitutus minor taxa was found than Yannggu and Inje. The correlation between the soil microorganism N-methylcytisine was analyzed. Among these microorganisms, Paraburkholderia had a positive correlation with N-methylcytisine. Meanwhile, Rhizomicrobium, CP011215_f (Paceibacter), KB906767_g (Solibacteres) and Opitutus negatively correlated with N-methylcytisine. The results suggested that soil microorganisms in the habitats influenced the variations of the N-methylcytisine.

Effect of Fecal Microbiota Transplantation on Non-Alcoholic Fatty Liver Disease: A Randomized Clinical Trial

Background and Aims

The clinical efficacy of fecal microbiota transplantation (FMT) in patients with non-alcoholic fatty liver disease (NAFLD) and the variant effects of FMT on lean and obese NAFLD patients remain elusive. Our study aimed to determine the clinical efficacy and safety of FMT for patients with NAFLD, elucidating its different influences on lean and obese patients with NAFLD.

Methods

We performed a randomized and controlled clinical trial. Patients in the non-FMT group were administered oral probiotics. In the FMT group, patients were randomized to receive FMT with donor stool (heterologous) via colonoscopy, followed by three enemas over 3 days. Both groups were also required to maintain a healthy diet and keep regular exercise for more than 40 min every day. They returned to the hospital for reexamination 1 month after treatment.

Results

FMT can decrease the fat accumulation in the liver by improving the gut microbiota dysbiosis, thus attenuating fatty liver disease. Significant differences in the clinical features and gut microbiota between lean and obese NAFLD patients were unveiled. Moreover, FMT had better effects on gut microbiota reconstruction in lean NAFLD than in obese NAFLD patients.

Conclusions

FMT could successfully improve the therapeutic effects on patients with NAFLD, and its clinical efficacy was higher in lean NAFLD than in obese NAFLD patients.

Characteristics and diversity of endophytic bacteria in Panax notoginseng under high temperature analysed using full-length 16S rRNA sequencing

Panax notoginseng is a traditional Chinese medicinal herb with diverse properties that is cultivated in a narrow ecological range because of its sensitivity to high temperatures. Endophytic bacteria play a prominent role in plant response to climate warming. However, the endophytic bacterial structures in P. notoginseng at high temperatures are yet unclear. In the present study, the diversity and composition of the endophytic bacterial community, and their relationships with two P. notoginseng plants with different heat tolerance capacities were compared using the full-length 16S rRNA PacBio sequencing system. The results revealed that the diversity and richness of endophytic bacteria were negatively associated with the heat tolerance of P. notoginseng. Beneficial Cyanobacteria, Rhodanobacter and Sphingomonas may be recruited positively by heat-tolerant plants, while higher amounts of adverse Proteobacteria such as Cellvibrio fibrivorans derived from soil destructed the cellular protective barriers of heat-sensitive plants and caused influx of pathogenic bacteria Stenotrophomonas maltophilia. Harmonious and conflicting bacterial community was observed in heat-tolerant and heat-sensitive P. notoginseng, respectively, based on the co-occurrence network. Using functional gene prediction of metabolism, endophytic bacteria have been proposed to be symbiotic with host plants; the bacteria improved primary metabolic pathways and secondary metabolite production of plants, incorporated beneficial endophytes, and combated adverse endophytes to prompt the adaptation of P. notoginseng to a warming environment. These findings provided a new perspective on the function of endophytes in P. notoginseng adaptation to high temperatures, and could pave the way for expanding the cultivable range of P. notoginseng.

Movements of southern elephant seals (Mirounga leonina) from Davis Base, Antarctica: combining population genetics and tracking data

Marine animals such as the southern elephant seal (Mirounga leonina) rely on a productive marine environment and are vulnerable to oceanic changes that can affect their reproduction and survival rates. Davis Base, Antarctica, acts as a moulting site for southern elephant seals that forage in Prydz Bay, but the mitochondrial haplotype diversity and natal source populations of these seals have not been characterized. In this study, we combined genetic and animal tracking data on these moulting seals to identify levels of mitochondrial haplotype diversity, natal source population, and movement behaviours during foraging and haul-out periods. Using partial sequences of the mitochondrial control region, we identified two major breeding mitochondrial lineages of seals at Davis Base. We found that the majority of the seals originated from breeding stocks within the South Atlantic Ocean and South Indian Ocean. One seal was grouped with the Macquarie Island breeding stock (South Pacific Ocean). The Macquarie Island population, unlike the other two stocks, is decreasing in size. Tracking data revealed long-distance foraging activity of the Macquarie Island seal around Crozet Islands. We speculate that changes to the Antarctic marine environment can result in a shift in foraging and movement strategies, which subsequently affects seal population growth rates.

Effects of Dietary Antimicrobial Growth Promoters on Performance Parameters and Abundance and Diversity of Broiler Chicken Gut Microbiome and Selection of Antibiotic Resistance Genes

Antimicrobial growth promoters (AGPs) are commonly used in broiler production. There is a huge societal concern around their use and their contribution to the proliferation of antimicrobial resistance (AMR) in food-producing animals and dissemination to humans or the environment. However, there is a paucity of comprehensive experimental data on their impact on poultry production and the AMR resistome. Here, we investigated the effect of five antimicrobial growth promoters (virginiamycin, chlortetracycline, bacitracin methyl disalicylate, lincomycin, and tylosin) used in the commercial broiler production in the Indian subcontinent and in the different parts of the world for three consecutive production cycles on performance variables and also the impact on gut bacteria, bacteriophage, and resistome profile using culture-independent approaches. There was no significant effect of AGPs on the cumulative growth or feed efficiency parameters at the end of the production cycles and cumulative mortality rates were also similar across groups. Many antibiotic resistance genes (ARGs) were ubiquitous in the chicken gut irrespective of AGP supplementation. In total, 62 ARGs from 15 antimicrobial classes were detected. Supplementation of AGPs influenced the selection of several classes of ARGs; however, this was not correlated necessarily with genes relevant to the AGP drug class; some AGPs favored the selection of ARGs related to antimicrobials not structurally related to the AGP. AGPs did not impact the gut bacterial community structure, including alpha or beta diversity significantly, with only 16-20 operational taxonomic units (OTUs) of bacteria being altered significantly. However, several AGPs significantly reduced the population density of some of the potential pathogenic genera of bacteria, such as Escherichia coli. Chlortetracycline increased the abundance of Escherichia phage, whereas other AGPs did not influence the abundance of bacteriophage significantly. Considering the evidence that AGPs used in poultry production can select for resistance to more than one class of antimicrobial resistance, and the fact that their effect on performance is not significant, their use needs to be reduced and there is a need to monitor the spread of ARGs in broiler chicken farms.

Changes in the Diversity and Composition of Gut Microbiota of Red-Crowned Cranes (Grus japonensis) after Avian Influenza Vaccine and Anthelmintic Treatment

Gut microbiota homeostasis is important for host health and well-being; however, drugs may affect the composition and function of the gut microbiota. Red-crowned cranes are a vulnerable species. Treatment of red-crowned cranes with avian influenza vaccines and anthelmintics has played pivotal roles in therapeutic management in zoos. To investigate the changes in the diversity and composition of gut microbiota after the avian influenza vaccine and anthelmintic treatment, we used 16S rRNA sequencing to obtain and compare the bacterial community composition before and after the treatment. The alpha diversity of the gut microbiota of red-crowned cranes decreased on the day of the treatment and then fluctuated over time. The composition of gut microbiota tended to be similar in the short term after the treatment, as supported by the beta diversity hierarchical cluster analysis. Only 3, 8, and 72 operational taxonomic units (OTUs) of the three individuals were shared among the five groups before and after treatment. The relative abundance of Firmicutes significantly increased to 99.04% ± 0.28% on the day of the treatment, in which the relative abundance of Lactobacillus was 93.33% ± 5.85%. KEGG pathways analysis indicated that the main function of the gut microbiota is involved in metabolism, and the present study indicates that the gut microbiota of red-crowned cranes is resilient to the avian influenza vaccine and anthelmintic, even disordered in the short term, and could recover over time. More individual experimentation and functional potential in metabolism are needed in the future to support animal disease control and optimal management in the zoo.

Effect of luxS encoding a synthase of quorum-sensing signal molecule AI-2 of Vibrio vulnificus on mouse gut microbiome

Autoinducer-2 (AI-2), a quorum-sensing signal molecule from the human pathogen Vibrio vulnificus, was assessed for its effect on the gut microbiome of mice. For this, we employed 16S rRNA sequencing to compare the gut microbiome of mice infected with either wild-type V. vulnificus or with the isotype ΔluxS that has a deletion in luxS which encodes the biosynthetic function of AI-2. The relative ratio of wild-type Vibrio species in the jejunum and ileum of mice infected with the wild type was significantly higher than that in mice infected with ΔluxS, suggesting that AI-2 plays an important role in the colonization of V. vulnificus in the small intestine. The bacterial composition in the gut of mice infected with ΔluxS comprises a higher proportion of Firmicutes, composed mainly of Lactobacillus, compared to the mice infected with wild-type cells. In the large intestine, Vibrio species were barely detected regardless of genetic background. Three Lactobacillus spp. isolated from fecal samples from mice infected with ΔluxS manifested significant antibacterial activities against V. vulnificus. Culture supernatants from these three species were dissolved by HPLC, and a substance in fractions showing inhibitory activity against V. vulnificus was determined to be lactic acid. Our results suggest that luxS in V. vulnificus affects not only the ability of the species to colonize the host gut but also its susceptibility to the growth-inhibiting activity of commensal bacteria including Lactobacillus. KEY POINTS: • Gut microbiomes of ΔluxS-infected and WT Vibrio-infected mice differed greatly. • Difference was most prominent in the jejunum and ileum compared to the duodenum or large intestine. • In the small and large intestines of mice, the relative proportions of Vibrio and Lactobacillus species showed a negative relationship. • Effector molecules produced by Lactobacillus in mouse gut inhibit Vibrio growth.

Influence of Pollen Dispersal and Mating Pattern in Domestication of Intermediate Wheatgrass, a Novel Perennial Food Crop

Intermediate wheatgrass (IWG) is a perennial forage grass that is currently being domesticated as a grain crop. It is a primarily wind-pollinated outcrossing species and expresses severe inbreeding depression when self-pollinated. Characterization of pollen dispersal, mating parameters, and change in genetic diversity due to pollen movement is currently lacking in IWG. In this study, we examined pollen dispersal in an IWG selection nursery by evaluating 846 progeny from 15 mother plants and traced their parentage to 374 fathers. A set of 2,500 genomic loci was used to characterize the population. We assigned paternity to 769 (91%) progeny and the average number of fathers per mother plant was 37, from an average of 56 progeny examined per mother. An extensive number (80%) of pollination events occurred within 10 m of the mother plants. Pollination success was not correlated with trait attributes of the paternal genotypes. Mating system analysis confirmed that IWG is highly outcrossing and inbreeding was virtually absent. Neither genetic diversity nor the genome-estimated trait values of progeny were significantly affected by pollinator distance. The distance of pollinator in an IWG breeding nursery therefore was not found to be a major contributor in maintaining genetic diversity. These findings reveal the pollen dispersal model in IWG for the first time and its effect on genetic diversity, which will be valuable in designing future IWG breeding populations. Information generated and discussed in this study could be applied in understanding gene flow and genetic diversity of other open-pollinated species.

Effects of Fermented Feed on the Growth Performance, Intestinal Function, and Microbiota of Piglets Weaned at Different Age

The beneficial function of fermented feed in livestock industry has been widely investigated. However, little is known about the effects of fermented feed on different weaned-day piglets. This study aimed to investigate the effects of fermented diet on the growth performance, intestinal function, and microbiota of piglets weaned at the age of 21 and 28 days. The results found that weaning on day 21 significantly increased (p < 0.05) average daily gain (ADG), and average daily feed intake (ADFI) (calculated based on wet weight and dry matter), while reduced (p < 0.05) feed to gain ratio (F:G), the activities of trypsin and lipase of jejunum and the villus height of ileum, compared with 28-days weaning. The protein levels of Occludin, Claudin-1, and ZO-1 of ileum in the groups weaning on day 21 were less (p < 0.05) than the groups weaning on day 28. Moreover, dietary supplementation with fermented diet upregulated (p < 0.05) the Occludin, Claudin-1, and ZO-1 proteins of ileum, compared with the groups treated with control diet both weaning on day 21 and 28. In addition, dietary supplementation with fermented diet decreased (p < 0.05) the relative abundance of Clostridia (class) and increased (p < 0.05) the Bacteroidia (class) level of cecal microbiota, compared with the groups treated with control diet both weaning on day 21 and 28. However, supplementation with fermented diet did not affect the concentrations of short-chain fatty acids in the cecum (p > 0.05). Therefore, our data suggest that the feed digestibility is improved in piglets weaned at 21 days, but intestinal barrier function is weaker than in piglets weaned at 28 days. However, compared with feeding control diet, supplementation with fermented diet both improved the feed conversion and intestinal barrier function of weaned piglets by modulating intestinal microbiota.

Bacterial Dynamics and Their Influence on the Biogeochemical Cycles in a Subtropical Hypereutrophic Lake During the Rainy Season

Lakes in subtropical regions are highly susceptible to eutrophication due to the heavy rainfall, which causes significant runoff of pollutants (e.g., nutrients) to reach surface waters, altering the water quality and influencing the microbial communities that regulate the biogeochemical cycles within these ecosystems. Lake Cajititlán is a shallow, subtropical, and endorheic lake in western Mexico. Nutrient pollution from agricultural activity and wastewater discharge have affected the lake's water quality, leading the reservoir to a hypereutrophic state, resulting in episodes of fish mortality during the rainy season. This study investigated the temporal dynamics of bacterial communities within Lake Cajititlán and their genes associated with the nitrogen, phosphorus, sulfur, and carbon biogeochemical cycles during the rainy season, as well as the influences of physicochemical and environmental variables on such dynamics. Significant temporal variations were observed in the composition of bacterial communities, of which Flavobacterium and Pseudomonas were the dominant genera. The climatological parameters that were most correlated with the bacterial communities and their functional profiles were pH, DO, ORP, turbidity, TN, EC, NH4 +, and NO3 -. The bacterial communities displayed variations in their functional composition for nitrogen, phosphorus, and sulfur metabolisms during the sampling months. The bacterial communities within the lake are highly susceptible to nutrient loads and low DO levels during the rainy season. Bacterial communities had a higher relative abundance of genes associated with denitrification, nitrogen fixation, assimilatory sulfate reduction, cysteine, SOX system, and all phosphorus metabolic pathways. The results obtained here enrich our understanding of the bidirectional interactions between bacterial communities and major biogeochemical processes in eutrophic subtropical lakes.

Different responses of bacteria and fungi to environmental variables and corresponding community assembly in Sb-contaminated soil

Bacterial communities in antimony (Sb) polluted soils have been well addressed, whereas the important players fungal communities are far less studied to date. Here, we report different responses of bacterial and fungal communities to Sb contamination and the ecological processes controlling their community assembly. Soil samples in the Xikuangshan mining area were collected and subjected to high through-put sequencing of 16S rRNA and ITS1 to investigate bacterial and fungal communities, respectively, along an Sb gradient. Sb speciation in the soil samples and other physicochemical parameters were analyzed as well. Bacterial communities were dominated by Deltaproteobacteria in the soil with highest Sb concentration, whereas Chloroflexi were dominant in the soil with lowest Sb concentration. Fungal communities in high-Sb soils were predominated by unclassified Fungi, whilst Leotiomycetes were dominant in low-Sb soil samples. Multivariate analysis indicated that Sb, pH and soil texture were the main drivers to strongly impact microbial communities. We further identified Sb-resistant microbial groups via correlation analysis. In total, 18 bacterial amplicon sequence variants (ASVs) were found to potentially involve in biogeochemical cycles such as Sb oxidation, sulfur oxidation or nitrate reduction, whereas 12 fungal ASVs were singled out for potential heavy metal resistance and plant growth promotion. Community assembly analysis revealed that variable selection contributed 100% to bacterial community assembly under acidic or high Sb concentration conditions, whereas homogeneous selection dominated fungal community assembly with a contribution over 78.9%. The community assembly of Sb-resistant microorganisms was mainly controlled by stochastic process. The results offer new insights into microbial ecology in Sb-contaminated soils, especially on the different responses of microbial communities under identical environmental stress and the different ecological processes underlining bacterial and fungal community assembly.

Endophytic bacterial and fungal community compositions in different organs of ginseng (Panax ginseng)

Panax ginseng (Panax ginseng C. A. Mey.) is a perennial herb of the genus ginseng, which is used as medicine with dried roots and rhizomes. With the deepening of research on ginseng, the chemical components and pharmacological effects of ginseng have gradually been discovered. Endophytes are beneficial to host plants. However, the composition of endophytes in different organs from ginseng is poorly elucidated. The report of ginsenoside production by endophytic microbes isolated from Panax sp., motivated us to explore the endophytic microbial diversity related to the roots, stems, and leaves. In this study, the V5-V7 variable region of endophytic bacteria 16S rRNA gene and V1 variable region of endophytic fungi ITS gene in different organs were analyzed by high-throughput sequencing. The diversity and abundance of endophytic microbes in the three organs are different and are affected by the organs. For example, the most abundant endophytic bacterial genus in roots was Mycobacterium, while, the stems and leaves were Ochrobactrum. Similarly, the fungal endophytes, Coniothyrium and Cladosporium, were also found in high abundance in stems, in comparison to roots and leaves. The Shannon index shows that the diversity of endophytic bacteria in roots is the highest, and the richness of endophytic bacterial was root > stem (p < 0.05). Principal coordinate analysis showed that there were obvious microbial differences among the three groups, and the endophytic bacterial composition of the leaves was closer to that of the roots. This study provides an important reference for the study of endophytic microorganisms in ginseng.

Genomic diversity and antimicrobial resistance of Campylobacter spp. from humans and livestock in Nigeria

Background

Campylobacter spp. are zoonotic pathogens, ubiquitous and are found naturally as commensals in livestock from where they can be transmitted to humans directly or through animal products. The genomic diversity and antimicrobial resistance profile of Campylobacter was investigated with a focus on C. jejuni and C. coli in humans and livestock (poultry and cattle) from Nigeria.

Methods

586 human stool samples and 472 faecal samples from livestock were cultured for thermophilic Campylobacter species on modified charcoal cefoperazone deoxycholate agar (mCCDA). Culture in combination with whole genome sequencing identified and confirmed the presence of Campylobacter in humans and animals from the study area. Further analysis of the sequences was performed to determine multilocus sequence types and genetic determinants of antimicrobial resistance to fluoroquinolone, betalactam, tetracycline and macrolide classes of antimicrobials.

Results

From the human stool samples tested, 50 (9%) were positive of which 33 (66%) were C. jejuni, 14 (28%) were C. coli while 3 (6%) were C. hyointestinalis. In livestock, 132 (28%) were positive. Thirty one (7%) were C. jejuni while 101 (21%) were C. coli. Whole genome sequencing and MLST of the isolates revealed a total of 32 sequence types (STs) identified from 47 human isolates while 48 STs were identified in 124 isolates from livestock indicating a population which was overall, genetically diverse with a few more dominant strains. The antimicrobial resistance profiles of the isolates indicated a higher prevalence of resistance in Campylobacter isolated from livestock than in humans. Generally, resistance was greatest for betalactams (42%) closely followed by fluoroquinolones (41%), tetracyclines (15%) and lastly macrolides (2%). Multidrug resistance to three or more antimicrobials was observed in 24 (13%) isolates from humans (n = 1, 4%) and chicken (n = 23, 96%).

Conclusions

This study has further contributed information about the epidemiology, genetic diversity and antimicrobial resistance profile of thermophilic Campylobacter in Nigeria.

Apple microbial communities and differences between two main Chinese producing regions

Microbes on fresh apples are closely associated with fruit disease, preservation and quality control. Investigation into the microbial communities on apples from different producing regions could reveal the microbial specificity and help disease prevention and quality control. In this paper, the apple surface microbes of forty-four samples from two main Chinese apple-producing regions, Bohai Bay (BHB) and the Loess Plateau (LP), were investigated by sequencing fungal internal transcribed spacer (ITS) and bacterial 16S rRNA hypervariable sequences. BHB and LP apples contained significantly different bacterial and fungal communities. BHB apples had a higher fungal diversity than LP apples. A total of 102 different fungal and bacterial taxonomies were obtained between apples from the two regions, in which 24 genera were predominant. BHB apples had higher phytopathogenic fungal genera, such as Tilletiopsis, Acremonium, Candida and Phoma, indicating the higher phytopathogenic risks of apples from the humid climate of the BHB region. LP apples contained more bacterial genera identified as gut microbes, indicating the potential risks of contaminating apples with foodborne pathogens in the arid environment of the LP. This study highlighted the environment-oriented microbial specificity on apples from two main apple-producing regions, and provided a basis for further investigation.

Alternations in the gut microbiota and metabolome with newly diagnosed unstable angina

Gut microbiota plays an important role in coronary heart disease, but its compositional and functional changes in unstable angina (UA) remain unexplored. We performed metagenomic sequencing of 133 newly diagnosed UA patients and 133 sex- and age-matched controls, and profiled the fecal and plasma metabolomes in thirty case-control pairs. The alpha diversity of gut microbiota was increased in UA patients: the adjusted odds ratios (ORs) per standard deviation increase in Shannon and Simpson indices were 1.30 (95% confidence interval, 1.01-1.70) and 1.36 (1.05-1.81), respectively. Two common species (depleted Klebsiella pneumoniae and enriched Streptococcus parasanguinis; P ≤ 0.002) and three rare species (depleted Weissella confusa, enriched Granulicatella adiacens and Erysipelotrichaceae bacterium 6_1_45; P ≤ 0.005) were associated with UA. The UA-associated gut microbiota was depleted in the pathway of L-phenylalanine degradation (P = 0.001), primarily contributed by Klebsiella pneumoniae. Consistently, we found increased circulating phenylalanine in UA patients (OR = 2.76 [1.17-8.16]). Moreover, S. parasanguinis was negatively correlated with fecal citrulline (Spearman's r_s = -0.470, P = 0.009), a metabolite depleted in UA patients (OR = 0.26 [0.08-0.63]). These findings are informative to help understand the metabolic connection between gut microbiota and UA.

Quantitative Biofacies Analysis to Identify Relationships and Refine Controls on Paleosol Development, Prince Creek Formation, North Slope Alaska, USA

Late Cretaceous coastal plain deposits of the Prince Creek Formation (PCF) offer a rare glimpse into an ancient, high-latitude, arctic greenhouse ecosystem for which there is no modern analog. Here, we employ quantitative biofacies analysis to explore the spatio-temporal variability in PCF palynomorph and microbiota assemblages from nine paleosol horizons exposed along the Colville River, North Slope, Alaska. Biofacies results provide insight into paleoenvironmental controls on the coastal plain ecosystem. Cluster and ordination analyses recognize five biofacies and the following two assemblage types: (1) fern and moss dominated assemblages and (2) algae dominated assemblages. Ordination arrays biofacies along environmental gradients related to soil moisture and marine influence. Fern and moss dominated biofacies from regularly water-logged paleosols along lake and swamp margins on the lower delta plain clearly segregated from algae dominated assemblages of periodically drier levee-overbank paleosols. These results support previous interpretations from the sedimentology, paleopedology, and geochemistry of PCF paleosols that suggest that fluctuations in the water table, related to seasonal river discharge and variations in topography and drainage, controlled soil development and vegetation growth across the coastal plain. This quantitative biofacies-based approach provides an independent predictive tool and cross-check for interpreting environmental conditions along any ancient coastal ecosystem.

Modeling population size independent tissue epigenomes by ChIL-seq with single thin sections

Recent advances in genome-wide technologies have enabled analyses using small cell numbers of even single cells. However, obtaining tissue epigenomes with cell-type resolution from large organs and tissues still remains challenging, especially when the available material is limited. Here, we present a ChIL-based approach for analyzing the diverse cellular dynamics at the tissue level using high-depth epigenomic data. "ChIL for tissues" allows the analysis of a single tissue section and can reproducibly generate epigenomic profiles from several tissue types, based on the distribution of target epigenomic states, tissue morphology, and number of cells. The proposed method enabled the independent evaluation of changes in cell populations and gene activation in cells from regenerating skeletal muscle tissues, using a statistical model of RNA polymerase II distribution on gene loci. Thus, the integrative analyses performed using ChIL can elucidate in vivo cell-type dynamics of tissues.

Effect of heavy metals pollution on the composition and diversity of the intestinal microbial community of a pygmy grasshopper (Eucriotettix oculatus)

Heavy metal pollution in the environment is mostly manifested as a multi-elemental compound pollution. The effect of the long-term exposure to heavy metal pollution on the gut microbes of insects has remained unknown. For the current work, the population of Eucriotettix oculatus living in mining areas around the Diaojiang River with a history of hundreds of years of pollution, was selected along with the similar species living in non-mining areas to conduct a comparative study of their gut microbes. The microbial communities were analyzed using 16S rRNA amplicon sequencing. The results showed Proteobacteria to be dominant among gut microbes of E. oculatus, but the abundance of Proteobacteria was significantly increased when the insects were exposed to the environment with heavy metal pollution. The symbiotic bacteria belonging to genus Wolbachia were found to be dominant among the insect population from the non-mining area group, while the pathogenic bacteria belonging to Aeromonas were dominant among the insect population of the mining area group. The diversity analysis showed that the gut microbial community diversity of E. oculatus was reduced in the heavy metal pollution habitat. The analysis of the differences in the gut microbial population and metabolic pathways of the two groups showed that the heavy metal pollution caused the increase in pathogenic bacteria among the gut microbes of E. oculatus, which might have a negative impact on the health of the host. At the same time, probiotics and the beneficial metabolism pathways were also found to increase and enhance, helping the host to resist the damage caused by heavy metal stress. This might be one of the strategies used by E. oculatus to adapt to heavy metal pollution.

Diversity of Groundwater Crustaceans in Wells in Various Geologic Formations of Southern Poland

Data on Crustacea from underground waters accessed through wells are limited in Poland. A recent study was undertaken to determine diversity and factors influencing the crustacean communities inhabiting wells drilled in three bedrocks, Jurassic limestone, Cretaceous marls and flysch. A total of 23 crustacean species and subspecies were recorded belonging to Copepoda, Ostracoda, Amphipoda and Bathynellacea. Only four species of low abundance, however, were stygobionts. Our studies showed that abundance and species number of Copepoda and Ostracoda were affected by bedrock geology (with higher abundances and species richness in wells of Cretaceous marls), and in the case of copepods, also by sampling season. Furthermore, this paper lists all species of Crustacea recorded from inland groundwater habitats of Poland based published over the last 133 years. The most species-rich group was Copepoda with 43 representatives (four stygobites), followed by Ostracoda and Amphipoda with a total of 37 and 12 species, respectively (each with nine stygobites). In addition, two species of Isopoda (one stygobite) and one Bathynellid appear in the checklist. The checklist identifies geographical (and environmental) gaps which require further research.

Environmental Factors Associated with the Eukaryotic Microbial Community and Microalgal Groups in the Mountain Marshes of South Korea

The diversity indices of eukaryotic microalgal groups in the Jeonglyeongchi, Waegok, and Wangdeungjae marshes of Mount Jiri, Korea, were measured using Illumina MiSeq and culture-based analyses. Waegok marsh had the highest species richness, with a Chao1 value of 828.00, and the highest levels of species diversity, with Shannon and Simpson index values of 6.36 and 0.94, respectively, while Wangdeungjae marsh had the lowest values at 2.97 and 0.75, respectively. The predominant species in all communities were Phagocata sibirica (Jeonglyeongchi, 68.64%), Aedes albopictus (Waegok, 34.77%), Chaetonotus cf. (Waegok, 24.43%), Eimeria sp. (Wangdeungjae, 26.17%), and Eumonhystera cf. (Wangdeungjae, 22.27%). Relative abundances of the microalgal groups Bacillariophyta (diatoms) and Chlorophyta (green algae) in each marsh were respectively: Jeonglyeongchi 1.38% and 0.49%, Waegok 7.0% and 0.3%, and Wangdeungjae 10.41% and 4.72%. Illumina MiSeq analyses revealed 34 types of diatoms and 13 types of green algae. Only one diatom (Nitzschia dissipata) and five green algae (Neochloris sp., Chlamydomonas sp., Chlorococcum sp., Chlorella vulgaris, Scenedesmus sp.) were identified by a culture-based analysis. Thus, Illumina MiSeq analysis can be considered an efficient tool for analyzing microbial communities. Overall, our results described the environmental factors associated with geographically isolated mountain marshes and their respective microbial and microalgal communities.

Rotifers of Bahia State, Brazil: News records and limitations to studies

A first checklist of Rotifera species in freshwater environments in Bahia State, in northeastern Brazil, is provided. The list includes sampling data from 26 aquatic environments (lotic and lentic) undertaken from 2010 to 2016. One hundred and fifty-five species were recorded, with 68 new records for the state. The family Brachionidae and Lecanidae were the most representative (54.8%). The greatest richness was recorded in the Colônia River (57 species). Those results reflect the low numbers of studies previously undertaken in the region, indicating more research needs to be focused on Rotifera biodiversity in Bahia, the fifth largest state in Brazil (567,295 km2) with large numbers of freshwater bodies.

Pyrosequencing and Taxonomic Composition of the Fungal Community from Soil of Tricholoma matsutake in Gyeongju

Tricholoma matsutake is an ectomycorrhizal fungus that has a symbiotic relationship with the root of Pinus densiflora. Soil microbial communities greatly affect the growth of T. matsutake, however, few studies have examined the characteristics of these communities. In the present study, we analyzed soil fungal communities from Gyeongju and Yeongdeok using metagenomic pyrosequencing to investigate differences in fungal species diversity, richness, and taxonomic composition between the soil under T. matsutake fruiting bodies (Sample 2) and soil where the fairy ring of T. matsutake was no longer present (Sample 1). The same spot was investigated three times at intervals of four months to observe changes in the community. In the samples from Yeongdeok, the number of valid reads was lower than that at Gyeongju. The operational taxonomic units of most Sample 2 groups were less than those of Sample 1 groups, indicating that fungal diversity was low in the T. matsutakedominant soil. The soil under the T. matsutake fruiting bodies was dominated by more than 51% T. matsutake. From fall to the following spring, the ratio of T. matsutake decreased. Basidiomycota was the dominant phylum in most samples. G-F1-2, G-F2-2, and Y-F1-2 had the genera Tricholoma, Umbelopsis, Oidiodendron, Sagenomella, Cladophialophora, and Phialocephala in common. G-F1-1, G-F2-1, and Y-F1-1 had 10 genera including Umbelopsis and Sagenomella in common. From fall to the following spring, the amount of phyla Basidiomycota and Mucoromycota gradually decreased but that of phylum Ascomycota increased. We suggest that the genus Umbelopsis is positively related to T. matsutake.

Geographical Isolation and Root-Associated Fungi in the Marine Terrains: A Step Toward Establishing a Strategy for Acquiring Unique Microbial Resources

This study aimed to understand whether the geo-ecological segregation of native plant species affects the root-associated fungal community. Rhizoplane (RP) and rhizosphere (RS) fungal microbiota of Sedum takesimense native to three geographically segregated coastal regions (volcanic ocean islands) were analyzed using culture-independent methods: 568,507 quality sequences, 1399 operational taxonomic units, five phyla, and 181 genera were obtained. Across all regions, significant differences in the phyla distribution and ratio were confirmed. The Chao's richness value was greater for RS than for RP, and this variance coincided with the number of genera. In contrast, the dominance of specific genera in the RS (Simpson value) was lower than the RP at all sites. The taxonomic identity of most fungal species (95%) closely interacting with the common host plant was different. Meanwhile, a considerable number of RP only residing fungal genera were thought to have close interdependency on their host halophyte. Among these, Metarhizium was the sole genus common to all sites. These suggest that the relationship between potential symbiotic fungi and their host halophyte species evolved with a regional dependency, in the same halophyte species, and of the same natural habitat (volcanic islands); further, the fungal community differenced in distinct geographical regions. Importantly, geographical segregation should be accounted for in national culture collections, based on taxonomical uniqueness.

Diversity and host assemblage of avian haemosporidians in different terrestrial ecoregions of Peru

Characterizing the diversity and structure of host–parasite communities is crucial to understanding their eco-evolutionary dynamics. Malaria and related haemosporidian parasites are responsible for fitness loss and mortality in bird species worldwide. However, despite exhibiting the greatest ornithological biodiversity, avian haemosporidians from Neotropical regions are quite unexplored. Here, we analyze the genetic diversity of bird haemosporidian parasites (Plasmodium and Haemoproteus) in 1,336 individuals belonging to 206 bird species to explore for differences in diversity of parasite lineages and bird species across 5 well-differentiated Peruvian ecoregions. We detected 70 different haemosporidian lineages infecting 74 bird species. We showed that 25 out of the 70 haplotypes had not been previously recorded. Moreover, we also identified 81 new host–parasite interactions representing new host records for these haemosporidian parasites. Our outcomes revealed that the effective diversity (as well as the richness, abundance, and Shannon–Weaver index) for both birds and parasite lineages was higher in Amazon basin ecoregions. Furthermore, we also showed that ecoregions with greater diversity of bird species also had high parasite richness, hence suggesting that host community is crucial in explaining parasite richness. Generalist parasites were found in ecoregions with lower bird diversity, implying that the abundance and richness of hosts may shape the exploitation strategy followed by haemosporidian parasites. These outcomes reveal that Neotropical region is a major reservoir of unidentified haemosporidian lineages. Further studies analyzing host distribution and specificity of these parasites in the tropics will provide important knowledge about phylogenetic relationships, phylogeography, and patterns of evolution and distribution of haemosporidian parasites.