Permutational Multivariate Analysis Research Articles

Responses of soil microbial communities and enzyme activities under nitrogen addition in fluvo-aquic and black soil of North China.

This research investigates the impact of long-term nitrogen (N) addition on fluvo-aquic and black soils in north China, with a focus on soil microbial communities and enzyme activities. In each site, there were three N fertilization treatments, i.e., control, moderate-N, and high-N. Phospholipid Fatty Acid Analysis was employed to analyze the microbial community composition, and enzyme activities related to N, carbon (C), and phosphorus (P) cycling were assessed. The results showed that increasing N fertilization levels led to higher soil organic carbon (SOC) and total N (TN) concentrations, indicating enhanced nutrient availability. N fertilization reduced soil pH across both soils, with a more pronounced acidification effect observed in the black soil. Across both soils, N addition increased maize yield, but the higher crop yield was attained in moderate-N rate compared with high-N rate. Microbial community composition analysis revealed that N fertilization induced shifts in the relative abundances of specific microbial groups. The black soil exhibited pronounced shifts in the microbial groups compared to the fluvo-aquic soil, i.e., decreased fungal abundance and fungi: bacteria ratio in response to N input. In addition, the application of N fertilizer led to an elevated ratio of gram-positive to gram-negative (GP:GN) bacteria, but this effect was observed only in black soil. N fertilization had an impact on the enzyme activities related to C, N, and P cycling in both soil types, but black soil showed more pronounced changes in enzyme activities. Permutational multivariate analysis of variance indicated that soil types rather than N fertilization mediated the response of the soil microbial community and enzyme activities. Partial least square path modeling demonstrated that soil pH was the only key driver impacting soil microbial groups and enzyme activities in both soils. In conclusion, our findings highlighted that N fertilization exerted more pronounced impacts on soil biochemical properties, microbial community composition, and enzyme activities in black soil furthermore, moderate N rate resulted in higher crop productivity over high N rate.

Quantifying ant diversity and community in a subalpine forest mosaic: a comparison of two methods

Sampling efficiency, composition and detection biases associated with pitfall-trap and sample plot (standardised hand-collecting) methods were compared at seven high montane sites at Lasha Mountain, Yunnan, China. Rarefaction-interpolation curves showed total species diversity and sample coverage from each method were undifferentiated. Permutational multivariate analysis of variance showed highly overlapping communities. However, of all species collected, just 53% of all species found were shared between the two methods; 30% were exclusive to sample plot samples and 17% were exclusive to pitfall traps. Modelled comparisons of species richness (alpha) and proportion of species from the population (beta diversity) showed differences between methods. Permutational multivariate analysis of variance blocked by site showed community composition differed between methods, defined largely by the presence of a few dominant species.Implications for insect conservation: Our findings suggest that results from the two methods cannot be directly compared and are imperfect substitutes to one another. For long-term monitoring of biodiversity in complex forest mosaic systems, we suggest integrating a suite of complementary methods to achieve more complete representation of ant composition and diversity.

Irrigation rather than fertilization drives the abundance, community structure and assembly process of soil denitrifiers

Fertilization and irrigation have significant impacts on soil nitrogen cycling and associated microbes, yet we have limited understanding on community structure and assembly process of soil denitrifiers. Here, we examined the abundance, diversity, composition, and assembly process of soil denitrifier communities harboring the nirS, nirK, and nosZ genes in soils under long-term (11 years) fertilization and irrigation managements. Our results indicated that irrigation significantly increased the abundance of nirS, nirK, and nosZ genes by 6.10–18.85, 2.36–2.85, and 4.85–6.16 times in the chemical fertilizer (NPK) treatments and by 1.02–13.68, 0.95–1.45, and 1.49–2.28 times in the manure (M) treatments compared to the corresponding control without irrigation (I0), respectively. Principal co-ordinates analysis (PCoA) and permutational multivariate analysis of variance (PERMANOVA) showed that fertilization had a more important role in altering the nosZ-type denitrifier community structure, while irrigation dominated in influencing the nirS- and nirK-type. Regardless of fertilization, irrigation shifted community assembly of the nirS-type denitrifier from deterministic process to stochastic process, while driving the nosZ-type from stochastic process to deterministic process. The nirK-type denitrifier was determined by stochastic process and was neither affected by fertilization nor irrigation. Network co-occurrence analysis showed that irrigation differently affected the community network complexity under NPK and M. One irrigation (I1) and two irrigations (I2) increased and decreased the network complexity, respectively, in the NPK treatments, while opposite results were found in M. Additionally, soil moisture and pH significantly (p < 0.05) correlated with the gene abundance, community structure, and assembly process of the denitrifiers. Overall, irrigation rather than fertilization greatly induced the changes in abundance, community structure, network structure, and assembly process of the denitrifiers via soil moisture and pH, highlighting the importance of irrigation in regulating soil denitrification associated microbes.

Effects of elevated carbon dioxide (CO2)and ozone (O3)concentrations on ectoenzyme activities in rice rhizospheric soil.

Rising atmospheric carbon dioxide (CO2) and ozone (O3) concentrations are the main global change drivers. Soil ectoenzymes play an important role in maintaining soil ecosystem services. Exploring the responses of soil ectoenzymes to elevated CO2 and O3 concentrations is important for combating global climate change. In this study, we simulated elevated CO2 concentrations (+200 μmol·mol-1, eCO2), elevated O3 concentrations (0.04 μmol·mol-1, eO3), and their combination (eCO2+eO3) in open-top chambers (OTCs), and investigated the responses of rhizospheric soil ectoenzyme activities. The results showed that eCO2 significantly increased the β-D-Glucosidase (βG) activity by 73.0%, and decreased that of polyphenol oxidase (PHO), peroxidase (PEO), and acid phosphatase (AP) by 48.9%, 46.6% and 72.9% respectively, but did not affect that of cellulose hydrolase (CBH) and β-N-Acetylglucosaminidase (NAG). eO3 significantly reduced the activities of CBH and AP by 34.2% and 30.4%, respectively. The activities of PHO and AP were reduced by 87.3% and 32.3% under the eCO2+eO3 compared with the control, respectively. Results of the principal coordinate analysis, permutation multivariate analysis of variance and redundancy analysis showed that both elevated CO2 and O3 significantly affected soil ectoenzyme activities, with stronger effects of elevated CO2 than elevated O3. Root nitrogen content, root carbon to nitrogen ratio, soil microbial biomass carbon and nitrate nitrogen were the main drivers of soil ectoenzyme activities under elevated CO2 and O3. Elevated O3 could partially neutralize the effects of elevated CO2 on soil ectoenzyme activities. In conclusion, elevated CO2 and O3 restrained the activities of most soil ectoenzyme, suggesting that climate change would threat soil ecosystem services and functions in the agroecosystem.

Association between Residential Greenness and Human Microbiota: Evidence from Multiple Countries.

Greenness, referring to a measurement of the density of vegetated land (e.g., gardens, parks, grasslands), has been linked with many human health outcomes. However, the evidence on greenness exposure and human microbiota remains limited, inconclusive, drawn from specific regions, and based on only modest sample size. We aimed to study the association between greenness exposure and human microbial diversity and composition in a large sample across 34 countries and regions. We explored associations between residential greenness and human microbial alpha-diversity, composition, and genus abundance using data from 34 countries. Greenness exposure was assessed using the normalized difference vegetation index and the enhanced vegetation index mean values in the month before sampling. We used linear regression models to estimate the association between greenness and microbial alpha-diversity and tested the effect modification of age, sex, climate zone, and pet ownership of participants. Differences in microbial composition were tested by permutational multivariate analysis of variance based on Bray-Curtis distance and differential taxa were detected using the DESeq2 R package between two greenness exposure groups split by median values of greenness. We found that higher greenness was significantly associated with greater richness levels in the palm and gut microbiota but decreased evenness in the gut microbiota. Pet ownership and climate zone modified some associations between greenness and alpha-diversity. Palm and gut microbial composition at the genus level also varied by greenness. Higher abundances of the genera Lactobacillus and Bifidobacterium, and lower abundances of the genera Anaerotruncus and Streptococcus, were observed in people with higher greenness levels. These findings suggest that residential greenness was associated with microbial richness and composition in the human skin and gut samples, collected across different geographic contexts. Future studies may validate the observed associations and determine whether they correspond to improvements in human health. https://doi.org/10.1289/EHP12186.

Sources of gut microbiota variation in a large longitudinal Finnish infant cohort.

Although the infant gut microbiota has been extensively studied, comprehensive assessment on the microbiota determinants including technical variables has not been performed in large infant cohorts. We studied the effect of 109 variables on the 16S rRNA gene amplicon-based gut microbiota profiles of infants sampled longitudinally from three weeks to two years of life in the Finnish HELMi birth cohort. Spot faecal samples from both parents were included for intra-family analyses, totalling to 7657 samples from 985 families that were evaluated for beta-diversity patterns using permutational multivariate analysis on Bray-Curtis distances, and differential abundance testing and alpha-diversity for variables of interest. We also assessed the effect of different taxonomic levels and distance methods. In time point-specific models, the largest share of variation explained, up to 2-6%, were seen in decreasing order for the DNA extraction batch, delivery mode and related perinatal exposures, defecation frequency and parity/siblings. Variables describing the infant gastrointestinal function were continuously important during the first two years, reflecting changes in e.g., feeding habits. The effect of parity/siblings on infant microbiota was modified by birth mode and exposure to intrapartum antibiotics, exemplifying the tight interlinkage of perinatal factors relevant for infant microbiota research. In total, up to 19% of the biological microbiota variation in the infant gut could be explained. Our results highlight the need to interpret variance partitioning results in the context of each cohort's characteristics and microbiota processing. Our study provides a comprehensive report of key factors associated with infant gut microbiota composition across the two first years of life in a homogenous cohort. The study highlights possible important future research areas and confounding factors to be considered. This research was supported by Business Finland, Academy of Finland, Foundation for Nutrition Research and the Doctoral Program in Microbiology and Biotechnology, University of Helsinki, Finland.

Babesa Sewage Treatment Plant as a vital artificial wetland habitat for a multitude of avian species

This study aimed to glean basic ecological aspects on diversity and abundance, temporal variation and guild composition of the birds at Babesa Sewage Treatment Plant (STP). The line transect method was used as the sampling technique from November 2021 to October 2022. A total of 80 species belonging to 58 genera, 29 families, and 11 orders were detected, of which three, namely, River Lapwing Vanellus duvaucelii, Falcated Duck Mareca falcata, and Ferruginous Duck Aythya nyroca, are ‘Near Threatened’ with the remaining being ‘Least Concern’. The highest species richness was recorded in the winter (6.29), the highest species diversity in the spring (2.73), and the highest evenness in the summer (0.76). There was not any statistically significant difference between non-waterbirds and waterbirds, or between feeding guilds. However, based on a permutational multivariate analysis of variance (PERMANOVA), the bird composition was significantly different among seasons. Subsequently, pairwise comparisons revealed a significant difference between autumn &amp; winter (P = 0.006), autumn &amp; summer (P = 0.006), autumn &amp; spring (P = 0.018), winter &amp; summer (P = 0.006), winter &amp; spring (P = 0.006) as well as spring &amp; summer (P = 0.006). The non-metric multidimensional scaling (NMDS) biplot showed most bird species overlap occurred between autumn and spring as well as summer and spring, respectively. Taken together, the present results suggest that the Babesa STP holds significant potential as a habitat for diverse avian populations and underscores the ecological significance of artificial wetlands.

Whistle characterization of long-beaked common dolphin (Delphinus delphis bairdii) in La Paz Bay, Gulf of California.

Long-beaked common dolphin (Delphinus delphis bairdii) distribution is limited to the Eastern North Pacific Ocean. Its whistle repertoire is poorly investigated, with no studies in the Gulf of California. The aim of the present study is to characterize the whistles of this species and compare their parameters with different populations. Acoustic monitoring was conducted in La Paz Bay, Gulf of California. Recordings were inspected in spectrogram view in Raven Pro, selecting good quality whistles (n = 270). In the software Luscinia, contours were manually traced to obtain whistle frequencies and duration. Number of steps, inflection points and contour type were visually determined. We calculated the descriptive statistics of the selected whistle parameters and we compared the results with a dolphins population from the Eastern Pacific Ocean. Permutational multivariate analysis of variance (PERMANOVA) was performed to test the intraspecific variation of the whistle parameters among groups. In the present study the mean values (±SD) of the whistle parameters were: maximum frequency = 14.13 ±3.71 kHz, minimum frequency = 8.44 ±2.58 kHz and duration = 0.44 ±0.31 s. Whistles with the upsweep contour were the most common ones (34.44%). The coefficient of variation (CV) values for modulation parameters were high (>100%), in accordance with other studies on dolphins. Whistle parameters showed significant differences among groups. Finally, ending and maximum frequencies, duration and inflection points of the whistles recorded in the present study were lower compared with the parameters of the long-beaked common dolphins from the Eastern Pacific Ocean. This study provides the first whistle characterization of long-beaked common dolphin from the Gulf of California and it will help future passive acoustic monitoring applications in the study area.

Oral and Gut Microbiota Dysbiosis is Associated with Mucositis Severity in Autologous Hematopoietic Stem Cell Transplantation: Evidence from an Asian Population

Mucositis is a debilitating complication of hematopoietic stem cell transplant (HSCT). It is unclear how changes in the composition of microbiota, which are modulated by geographical location and ethnicity, may influence immune regulation leading to the development of mucositis, and the study of both oral and gut microbiota in a single population of autologous HSCT in the Asian region is lacking. The study aimed to characterize the oral and gut microbiota changes, and the impact on both oral and lower gastrointestinal (GI) mucositis, with its associated temporal changes in a population of adult autologous HSCT. Autologous HSCT patients aged 18 years old and above were recruited from Hospital Ampang, Malaysia, between April 2019 to December 2020. Mucositis assessments were conducted daily, whilst blood, saliva and fecal samples were collected prior to conditioning regimen, on Day 0, Day+7 and 6-month post-transplant. Longitudinal differences in alpha and beta diversities were determined using Wilcoxon signed-rank test and Permutational Multivariate Analysis of Variance, respectively. Changes in relative abundances of bacteria across timepoint were assessed using the Microbiome Multivariate Analysis by Linear Models function. The combined longitudinal effects of clinical, inflammatory and microbiota variables on mucositis severity were measured using the generalized estimating equation. From the 96 patients analyzed, oral mucositis and diarrhea (representing lower GI mucositis) were reported at 58.3% and 95.8%, respectively. Alpha and beta diversities were significantly different between sample types (p<0.001) and across timepoints, with alpha diversity reaching statistical significance at Day 0 in fecal (p<0.001) and Day+7 in saliva samples (p<0.001). Diversities normalized to baseline by 6-month. Significant microbiota, clinical and immunological factors were associated with increasing mucositis grades. Increasing relative abundances of saliva Paludibacter, Leuconostoc and Proteus, were associated with higher oral mucositis grades, whilst increasing relative abundances of fecal Rothia and Parabacteroides were associated with higher GI mucositis grades. Meanwhile, increasing relative abundances of saliva Lactococcus and Acidaminococcus, and fecal Bifidobacterium were associated with protective effects against worsening oral and GI mucositis grades, respectively. This study provides real-world evidence and insights into the dysbiosis of the microbiota in patients exposed to conditioning regimen during HSCT. Independent of clinical and immunological factors, we demonstrated significant associations between relative bacteria abundances with the increasing severities of oral and lower GI mucositis. The findings presented in our study offer a potential rationale to consider the inclusion of preventive and restorative measures targeting oral and lower GI dysbiosis as interventional strategies to ameliorate mucositis outcome in HSCT patients.

Prenatal physical activity and the gut microbiota of pregnant women: results from a preliminary investigation.

To determine whether physical activity (PA), specifically meeting the recommended 150 minutes of moderate-intensity PA per week, is associated with gut microbiota composition in pregnant women. In an ongoing birth cohort study, questions from the Behavioral Risk Factor Surveillance System, which provides data on PA variables, were used to determine whether pregnant women met or exceeded the PA recommendations. To profile the composition of gut bacterial microbiota, 16S rRNA sequencing was performed on stool samples obtained from pregnant women. Differences in alpha diversity metrics (richness, Pielou's evenness, and Shannon's diversity) according to PA were determined using linear regression, whereas beta diversity relationships (Canberra and Bray-Curtis) were assessed using Permutational multivariate analysis of variance (PERMANOVA). Differences in relative taxon abundance were determined using DESeq2. The complete analytical sample included 23 women that were evaluated for both PA and 16S rRNA sequencing data (median age [Q1; Q3] = 30.5 [26.6; 34.0] years; 17.4% Black), and 11 (47.8%) met or exceeded the PA recommendations. Meeting or exceeding the PA recommendations during pregnancy was not associated with gut microbiota richness, evenness, or diversity, but it was related to distinct bacterial composition using both Canberra (p = 0.005) and Bray-Curtis (p = 0.022) distances. Significantly lower abundances of Bacteroidales, Bifidobacteriaceae, Lactobacillaceae, and Streptococcaceae were observed in women who met or exceeded the PA recommendations (all false discovery rates adjusted, p &lt; 0.02). Pregnant women who met or exceeded the PA recommendations showed altered gut microbiota composition. This study forms the basis for future studies on the impact of PA on gut microbiota during pregnancy.

Food tree selection by an arboreal marsupial: Implications for timber harvest

ContextThe Yellow-bellied Glider (Petaurus australis) is a vulnerable arboreal Australian marsupial that is threatened by logging. Trees used for sap feeding (sap trees) are a critical habitat requirement of the species, yet no harvest retention policy exists in the southern part of its range in Victoria, Australia. Yellow-bellied Gliders are extremely selective in sap tree use with some trees used far more frequently than others. AimsWe aimed to determine the tree species used and identify characteristics influencing intra-species tree selection for sap feeding by Yellow-bellied Gliders in the Highlands - Southern Fall Bioregion of Victoria. MethodsSap trees were located at each of 12 sites. We measured nine characteristics related to photosynthetic capability, microsite, and habitat for sap trees and the nearest tree of the same species without Yellow-bellied Glider incisions (reference tree). For sap trees, we measured 11 incision-related variables. Permutational Multivariate Analysis of Variance was conducted to identify distinguishing characteristics of sap trees. Generalised Linear Mixed Modelling was used to determine the influence of tree characteristics on abundance of incisions on a tree. Key resultsFive of 24 tree and tall shrub species present across the 12 sites were used for sap feeding. All five species were Eucalyptus. Within the tree species used, Yellow-bellied Gliders selected for trees that were larger, had wider crowns and occupied dominant and co-dominant canopy positions. ConclusionsYellow-bellied Gliders are highly selective of trees used for sap feeding. Although primarily selecting larger more dominant trees for sap feeding, lack of clear identifying characteristics means that identifying and retaining preferred sap trees in logging coupes must rely on site surveys for incisions on trees.

The newcomer takes it all: the invader Texas citrus mite, Eutetranychus banksi (Acari: Tetranychidae), displaces the resident relatives in citrus agrosystems

Many studies have emphasized the importance of interspecific competition in shaping natural ecosystem communities. In contrast, few investigations have explored the role of competition in agricultural environments after the arrival of an invasive pest species. We evaluated the ecological impact produced by the invasive Texas citrus mite, Eutetranychus banksi (McGregor), on the resident spider mites Panonychus citri (McGregor) and Eutetranychus orientalis (Klein) on the main citrus crop area in Eastern Spain. Since its arrival in 2013, E. banksi has become the most common and abundant spider mite on citrus, apparently leading to a reduction in the presence and geographic range of the other related species. Competitive relationships were detected between E. banksi–E. orientalis and E. banksi–P. citri pairs using co-occurrence analysis. Furthermore, generalized linear model analysis showed that the probability of finding E. orientalis or P. citri decreases with increasing E. banksi density and vice versa. Principal component analysis and permutational multivariate analysis of variance found competition between these two pairs, and also between the E. orientalis–P. citri pair. Redundancy and variation partitioning analysis revealed how the geographic distribution of the three spider mites is not caused by the environmental conditions, but it is strongly influenced by their colonization history and competitive relationships, since the areas with the highest density of the three species are related to their place of first detection, and do not coincide geographically. Finally, the mechanisms that may be involved in the competitive displacement and the possible future scenarios are discussed.

Intertidal macroalgal and epiphytic polychaete distributions strengthen marine ecoregions of Western Australia

The Marine Ecoregions of the World system separates the oceans into 232 ecoregions based on coastal and shelfwater species distributions. We tested the separation of those ecoregions and delineated subecoregions within Western Australian waters using intertidal macroalgal and epiphytic polychaete distributions. Environmental predictors of those assemblages were also determined. We collected macroalgae and polychaetes on 38 rocky intertidal shores within four marine ecoregions from 18°S to 34°S: (1) Exmouth to Broome, (2) Ningaloo, (3) Houtman, and (4) Leeuwin. We evaluated differences in species composition of macroalgae and polychaetes among those ecoregions using pairwise permutational multivariate analysis of variance and delineated subecoregions within each ecoregion using hierarchical cluster analysis. Multivariate relationships between environmental variables and assemblages were determined using distance-based linear models. The species composition of macroalgae and polychaetes significantly differed among ecoregions, with dissimilarity of 78-96% for macroalgae and 62-75% for polychaetes. We identified three subecoregions within Exmouth to Broome and Ningaloo and two subecoregions within Houtman and Leeuwin based on macroalgal distribution. We also found two subecoregions within Houtman and no subecoregion within Exmouth to Broome, Ningaloo, and Leeuwin based on polychaete distribution. Environmental predictors could explain 51% of the total variation of macroalgae and 41% of the total variation of polychaetes. The top two predictors explaining a high proportion of assemblage distribution were sea surface temperature (15% for macroalgae and 12% for polychaetes) and tidal amplitude (10% for macroalgae and 6% for polychaetes). These ecoregions and subecoregions can be used as an alternative spatial framework for classifying rocky intertidal habitats for designing marine protected area networks within Western Australian waters.

Landscape heterogeneity drives spatial distribution of palm community in a Neotropical rainforest reserve affected by defaunation

Background: Our study presents the first assessment of the relationships between environmental heterogeneity and the palm community at the landscape scale at the northern boundary of tropical rainforest distribution in America.&#x0D; Question: How does landscape-level heterogeneity (edaphic, topographic as well as the density, diversity, and tree biomass) shapes the palm community in a protected reserve affected by defaunation?&#x0D; Study site and date: The study was carried out in Los Tuxtlas Tropical Biology Station, Veracruz, Mexico (2020).&#x0D; Methods: We delineated landscape units (LUs) based on soil and geomorphology to characterize the biophysical mosaic. We built rank-abundance curves to compare the palm richness and their abundance among LUs. Permutational multivariate analysis of variance (PERMANOVA) and nonmetric multidimensional scaling (NMDS) were applied to detect shifts in the palm community across LUs.&#x0D; Results: Integrating abiotic and biotic components by delimiting LUs allowed us to evaluate the multifactorial effect of environmental heterogeneity on the palm community. The density and composition of the palms changed significantly among the LUs, influenced by soil coarse fragments, elevation, slope inclination, and annual precipitation. Tree richness and density had a significant effect on the palm community only when analyzed in combination with the soil-topography variables.&#x0D; Conclusions: The results reveal that there is high edaphic and topographic heterogeneity that influences palm species distribution at the landscape scale. The environmental heterogeneity approach allows capturing novel abiotic variation to explain the distribution patterns of palm species and their coexistence in highly diverse tropical communities.

Does PM1 exposure during pregnancy impact the gut microbiota of mothers and neonates?

BackgroundAmbient air pollutant exposure can change the composition of gut microbiota at 6-months of age, but there is no epidemiological evidence on the impacts of exposure to particulate matter with an aerodynamic diameter ≤1 μm (PM1) during pregnancy on gut microbiota in mothers and neonates. We aimed to determine if gestational PM1 exposure is associated with the gut microbiota of mothers and neonates. MethodsLeveraging a mother-infant cohort from the central region of China, we estimated the exposure concentrations of PM1 during pregnancy based on residential address records. The gut microbiota of mothers and neonates was analyzed using 16 S rRNA V3–V4 gene sequences. Functional pathway analyses of 16 S rRNA V3–V4 bacterial communities were conducted using Tax4fun. The impact of PM1 exposure on α-diversity, composition, and function of gut microbiota in mothers and neonates was evaluated using multiple linear regression, controlling for nitrogen dioxide (NO2) and ozone (O3). Permutation multivariate analysis of variance (PERMANOVA) was used to analyze the interpretation degree of PM1 on the sample differences at the OTU level using the Bray-Curtis distance algorithm. ResultsGestational PM1 exposure was positively associated with the α-diversity of gut microbiota in neonates and explained 14.8% (adj. P = 0.026) of the differences in community composition among neonatal samples. In contrast, gestational PM1 exposure had no impact on the α- and β-diversity of gut microbiota in mothers. Gestational PM1 exposure was positively associated with phylum Actinobacteria of gut microbiota in mothers, and genera Clostridium_sensu_stricto_1, Streptococcus, Faecalibacterium of gut microbiota in neonates. At Kyoto Encyclopedia of Genes and Genomes pathway level 3, the functional analysis results showed that gestational PM1 exposure significantly down-regulated Nitrogen metabolism in mothers, as well as Two-component system and Pyruvate metabolism in neonates. While Purine metabolism, Aminoacyl-tRNA biosynthesis, Pyrimidine metabolism, and Ribosome in neonates were significantly up-regulated. ConclusionsOur study provides the first evidence that exposure to PM1 has a significant impact on the gut microbiota of mothers and neonates, especially on the diversity, composition, and function of neonatal meconium microbiota, which may have important significance for maternal health management in the future.

Two centuries of spatial and temporal dynamics of freshwater fish introductions

AbstractAimInvestigating major freshwater fish flows (translocations) between biogeographic regions and their temporal dynamics and also quantifying spatial patterns and temporal changes in the array of introduced species, and the emergence and distance between major donor and recipient regions.LocationGlobal.Time Period1800–2020.Major Taxa StudiedFreshwater fishes.MethodsWe analysed a global dataset on freshwater fish introductions (4241 events of 688 species). Freshwater fish flows were investigated with flow diagrams and χ2 tests, while PERMANOVA (permutational multivariate analysis of variance) was used to test the association between species and regions and temporal shifts. Cluster analysis revealed major recipient areas and composition of the introduced species. Finally, changes in distances between donor and recipient sites were tested with PERMANOVA.ResultsThe number of introductions between biogeographic regions mirrored the European and North American dominance before World War II (WWII) and the trends in recreational fishing, biocontrol programmes and food production, especially in the Sino‐Oriental region, which has a long tradition of aquaculture and fishkeeping. Over the years, the origins and composition of introduced species changed uniquely in each biogeographic region, although the most introduced species are common to every region. Salmonids and other cold‐water species were frequently introduced before the 1950s, whereas tropical ornamental and aquaculture species currently prevail. Distances between donor and recipient sites did not vary over the time. After WWII, the Sino‐Oriental region consolidated its dominance and the Ethiopian and Neotropical regions emerged as new global donor and recipient regions.Main ConclusionsGlobal policy should focus on tropical ornamental and aquaculture species, which could benefit from global warming, especially in the Sino‐Oriental region, because it currently dominates freshwater fish species flows, and the Ethiopian and Neotropical regions, because they recently emerged as important global donor and recipient regions of freshwater fish introductions.

Temporal community structure and seasonal climatic migration of coastal sharks and large teleost fishes in the northeast Gulf of Mexico

We conducted monthly fishery-independent sampling using scientific gillnets and longlines at two seagrass shoals and surrounding soft-bottom habitat in the northeast Gulf of Mexico. Using non-metric multidimensional scaling, we explored the effects of abiotic variables on temporal patterns of fish community structure, analyzed temporal patterns using permutational multivariate analysis of variance, and tested for cyclicity in community structure. Additionally, we used generalized additive models to explore the effects of environmental variables on immigration and emigration phases of dominant taxa. We found strong seasonality and cyclicity in assemblages captured by both gear types, with depauperate winter communities and diverse assemblages in warmer month. Our results suggest that temperature may determine the timing of immigration and duration of the residency period of dominant taxa, but photoperiod may cue immigration and emigration in adults when the purpose of those migrations includes predicable reproductive functions (e.g., parturition). We found evidence of partial migration in juvenile life stages of some coastal sharks and hypothesize that rising temperatures due to climate change may have variable effects on residency patterns over ontogeny.

Amplicon-based metagenomic association analysis of gut microbiota in relation to egg-laying period and breeds of hens

BackgroundThe gut microbiota plays an essential role in maintaining gut homeostasis and improving performance, with the composition of microbial communities visibly differing across different laying stages in hens and significantly correlating with egg production. To gain further insights into the association between microbial community characteristics and laying periods in Hy-Line variety brown and Isa brown laying hens, we conducted a 16S rRNA amplicon sequencing survey.ResultsOur result revealed the diversity of bacteria in the early laying period was commonly higher than peak, and in Hy-Line variety brown laying hens were generally higher than Isa brown. Principal coordinate analysis (PCoA) and permutational multivariate analysis of variance (PERMANOVA) revealed that the structure and composition of the gut microbiota of laying hens exhibited significant differences among different groups. Phylum Firmicutes, Bacteroidota, Proteobacteria, and Fusobacteriota were found that dominant in the host’s feces. Therein, the abundance of Fusobacteriota was higher in the peak period than in the early period, while the abundance of Cyanobacteria in the early period was higher in two breeds of hens. Furthermore, random forest based on machine learning showed that there were several distinctly abundant genera, which can be used as potential biomarkers to differentiate the different groups of laying periods and breeds. In addition, the prediction of biological function indicated the existing discrepancy in microbial function among the microbiota of four groups.ConclusionsOur findings offer new insights into the bacterial diversity and intestinal flora composition of different strains of laying hens during various laying periods, contributing significantly to the improvement of production performance and the prevention of chicken diseases.

Temporal population structure of rubber tree powdery mildew pathogen Erysiphe quercicola in Hainan, China

AbstractRubber tree powdery mildew, caused by the obligate pathogen Erysiphe quercicola, is a major threat to rubber tree plantations worldwide. To investigate the temporal changes in the population structure of E. quercicola, diseased samples were collected at three disease epidemic stages (overwinter, early epidemic and late epidemic) from three counties in Hainan, China. Population structure was assessed using 16 polymorphic microsatellite markers. Both permutational multivariate analysis of variance (PERMANOVA) and analysis of molecular variance (AMOVA) indicated that there were significant differences among the population structure of E. quercicola at different epidemic stages. Furthermore, the late epidemic populations had higher genetic diversity than the other two stages. Discriminant analysis of principal components (DAPC) and STRUCTURE analysis showed that E. quercicola samples grouped into four clusters. One of the clusters included only samples from the late epidemic stage, while the other three clusters included samples from all three sample stages. Further analysis confirmed that there were significant (p = 0.001) genetic differences among these four clusters. As the teleomorph stage of E. quercicola has not yet been reported on rubber tree, these findings suggest that the epidemic of rubber tree powdery mildew is not only established by local inoculum sources, but also may be by inoculum drifting from other plantations or through host jumps from other hosts.

6 Effect of sampling and storage conditions upon equine fecal microbial community

Equine feces offer a non-invasive sample which can provide an indication of the microbial community structure of part of the hindgut; however, microbial communities may be altered by technical artifacts introduced under field conditions. Four types of preservation method (preservation buffer (NAP), treatment with chlorhexidine digluconate, FTA card sample collection, cold (buffer-free) storage with insulated ice packs (COLD)) and time at ambient temperature (0, 24, 48, 72 h), were tested for their effect upon the microbial community structure of fecal samples from n = 5 mature, mixed breed horses, collected immediately post defecation. Sequencing of the 16S rRNA gene was performed using the Qiagen QIAseq 16S/ ITS screening panel and Illumina MiSeq sequencing platform. Alpha diversity was estimated using Shannon, Simpson, Chao1 and Observed diversity metrics, and compared using Kruskal-Wallis’ test (P < 0.05) and post hoc Dunn's test with Bonferroni adjustment. Bray Curtis distances and permutational multivariate ANOVA were used to assess β-diversity. There were significant differences in α-diversity with preservation method, but not with time at ambient storage or individual. Alpha diversity was significantly lower in FTA card samples compared with COLD samples for Shannon and Simpson, but not Chao1 or Observed metrics. All α-diversity metrics were significantly lower in FTA card samples compared with those in NAP (Table 1). No significant differences in α-diversity were identified for other comparisons. Regarding β-diversity, individual pony (P = 0.001), and time at ambient storage (P = 0.004) were significant and explained most of variance between samplesacross the study. Preservation method significantly influenced β-diversity as the second term in an additive model, after accounting for variance driven by individual pony (P = 0.011). These results highlight the strength of inter-individual variability and suggest that minimizing sample time at ambient temperature remains important for preserving the microbial composition of equine fecal samples. While preservation method may not have drastically affected the composition of dominant taxa across samples, microbial diversity was not fully preserved by FTA cards. This study identified a selection of comparably effective sample collection conditions which preserve microbial diversity in equine fecal samples.