Distance-based Redundancy Analysis Research Articles

Contrasting pollution responses of native and non-native fish communities in anthropogenically disturbed estuaries unveiled by eDNA metabarcoding

Understanding the influence of environmental pollutants on the assembly mechanisms of estuarine fish communities is vital for addressing conservation challenges in these biodiverse ecosystems. Although significant research has explored the toxic impacts of pollutants such as petroleum, heavy metals, and eutrophication on individual species and populations, their effects on community assembly processes and the differential responses of native versus non-native fish at the meta-community level remain inadequately understood. This study utilized environmental DNA (eDNA) metabarcoding to analyze fish community diversity across 28 subtropical estuaries in China, assessing how these pollutants affect community composition and assembly mechanisms. Results indicated that eDNA was 2.54 times more effective than traditional methods in species identification, while also enabling the detection of a higher number of non-native fish species and more diverse functional guilds within estuarine ecosystems. A significant distance decay pattern (p < 0.05) was observed among native fish, whereas non-native species exhibited non-significant patterns. Neutral and null models showed that non-native species had significantly higher migration rates (0.005939 vs 0.001757) and a greater contribution of stochastic processes (82.38% vs 70.59%) compared to native species. Additionally, distance-based redundancy analysis (db-RDA), variance partitioning analysis (VPA), and correlation analyses revealed that native species were strongly constrained by environmental factors, particularly oil, Hg, Zn, Pb, Cr6+, and NH4+, while non-native species displayed notable resilience to these pollutants. These findings highlight the potential for non-native species to disproportionately influence community dynamics and assembly through unrestricted random dispersal amid environmental disturbances. This research clarifies the contrasting ecological responses of native and non-native fish communities to anthropogenic pressures in estuarine environments, offering essential insights into ecosystem resilience and informing biodiversity conservation strategies in rapidly changing coastal ecosystems.

Relationships between microbial characteristics and the arsenic cycle in high-arsenic groundwater

Abstract Microbial activities play a pivotal role in the migration and transformation of arsenic (As) within groundwater systems, particularly at high concentrations. Focusing on the Kuitun River Basin, this study used high-throughput sequencing to unravel the intricate diversity of microbial communities and their influence on As enrichment. Groundwater with elevated As hosted richer and more diverse microbial populations compared to that with lower As levels. The Sobs and Shannon diversity indices for the high-As group initially declined before rising with increasing As concentrations. Key microbial taxa dominating these ecosystems included Pseudomonas, Acinetobacter, Aquabacterium, Novosphingobium, and Sphingobium, with Pseudomonas showing substantial variation in abundance across different As concentrations. Distance-based redundancy analysis emphasized the importance of dissolved oxygen in shaping the microbial landscape, followed closely by the interplay between iron and As concentrations. Flavobacteriaceae and Burkholderiaceae displayed inverse correlations with As levels, highlighting the multifaceted relationship between microbial communities and groundwater chemistry. This investigation underscores the profound impact of As concentration gradients on microbial biodiversity and elucidates a complex regulatory framework where environmental parameters and microorganisms collaborate in governing As accumulation in groundwater. The results enrich our understanding of the biogeochemical dynamics underlying arsenic behavior in subterranean aquatic habitats.

Adaptation of rhizobacterial and endophytic communities in Citrus Grandis Exocarpium to long-term organic and chemical fertilization.

Organic fertilizers (OF) are crucial for enhancing soil quality and fostering plant growth, offering a more eco-friendly and enduring solution compared to chemical fertilizers (CF). However, few studies have systematically analyzed the effects of OF/CF on root microbiome of medicinal plants, especially in combination with active ingredients. In this study, we investigated the composition and function of bacteria and fungi in the rhizosphere or within the root of traditional Chinese medicinal plants, Citri Grandis Exocarpium (Huajuhong), which were treated with OF or CF over 1, 3, and 5 years (starting from 2018). Additionally, we conducted metabolome analysis to evaluate the effects of different fertilizers on the medicinal properties of Huajuhong. The results indicated that extended fertilization could enhance the microbial population and function in plant roots. Notably, OF demonstrated a stronger influence on bacteria, whereas CF enhanced the cohesion of fungal networks and the number of fungal functional enzymes, and even potentially reduced the proliferation of harmful rhizosphere pathogens. By adopting distancebased redundancy analysis, we identified the key physicochemical characteristics that significantly influence the distribution of endophytes, particularly in the case of OF. In contrast, CF was found to exert a more pronounced impact on the composition of the rhizosphere microbiome. Although the application of OF resulted in a broader spectrum of compounds in Huajuhong peel, CF proved to be more efficacious in elevating the concentrations of flavonoids and polysaccharides in the fruit. Consequently, the effects of long-term application of OF or CF on medicinal plants is different in many ways. This research provides a guide for OF/CF selection from the perspective of soil microecology and aids us to critically assess and understand the effects of both fertilizers on the soil environment, and promotes sustainable development of organic agriculture.

Mangrove afforestation as an ecological control of invasive Spartina alterniflora affects rhizosphere soil physicochemical properties and bacterial community in a subtropical tidal estuarine wetland

Background The planting of mangroves is extensively used to control the invasive plant Spartina alterniflora in coastal wetlands. Different plant species release diverse sets of small organic compounds that affect rhizosphere conditions and support high levels of microbial activity. The root-associated microbial community is crucial for plant health and soil nutrient cycling, and for maintaining the stability of the wetland ecosystem. Methods High-throughput sequencing was used to assess the structure and function of the soil bacterial communities in mudflat soil and in the rhizosphere soils of S. alterniflora, mangroves, and native plants in the Oujiang estuarine wetland, China. A distance-based redundancy analysis (based on Bray–Curtis metrics) was used to identify key soil factors driving bacterial community structure. Results S. alterniflora invasion and subsequent mangrove afforestation led to the formation of distinct bacterial communities. The main soil factors driving the structure of bacterial communities were electrical conductivity (EC), available potassium (AK), available phosphorus (AP), and organic matter (OM). S. alterniflora obviously increased EC, OM, available nitrogen (AN), and NO3−-N contents, and consequently attracted copiotrophic Bacteroidates to conduct invasion in the coastal areas. Mangroves, especially Kandelia obovata, were suitable pioneer species for restoration and recruited beneficial Desulfobacterota and Bacilli to the rhizosphere. These conditions ultimately increased the contents of AP, available sulfur (AS), and AN in soil. The native plant species Carex scabrifolia and Suaeda glauca affected coastal saline soil primarily by decreasing the EC, rather than by increasing nutrient contents. The predicted functions of bacterial communities in rhizosphere soils were related to active catabolism, whereas those of the bacterial community in mudflat soil were related to synthesis and resistance to environmental factors. Conclusions Ecological restoration using K. obovata has effectively improved a degraded coastal wetland mainly through increasing phosphorus availability and promoting the succession of the microbial community.

Short-term warming decreased soil DOM content and microbial species in alpine wetlands but increased soil DOM content and hydrolase activity in alpine meadows on the Tibetan Plateau

As important carbon sinks, alpine wetlands on the Tibetan Plateau are undergoing severe degradation. To reveal warming-induced ecological shifts in alpine environments, this study determined soil nutrient contents, enzyme activities, absorption and fluorescence spectra and quadrupole time-of-flight mass spectra (metabolomes) of dissolved organic matter (DOM) and metagenomes based on short-term incubation (0 °C, 10 °C and 20 °C) of topsoil from alpine wetlands and meadows (degraded wetlands). Compared with meadows, wetlands had higher contents of soil DOM (dissolved organic carbon, dissolved organic nitrogen and dissolved phosphorous) and greater activities of hydrolases (β-glucosidase, cellobiohydrolase, β-N-acetylglucosaminidase and acid phosphatase), with those parameters all being highest at 20 °C in meadows and showing various dynamics in wetlands. Soil DOM in wetlands presented the lowest values of specific ultraviolet absorbances (SUVA254 and SUVA260) at 0 °C and the highest values at 10 °C, whereas the opposite was true in the meadows. Wetland soils had greater diversities of DOM molecular compositions and microbial communities, with warming gradually increasing the number of identified DOM compounds in meadows and decreasing the number of microbial species in both soils. Wetland soils had more Proteobacteria (44.2%) and Acidobacteria (21.1%) and fewer Actinobacteria (18.0%) than meadow soils and contained many temperature-sensitive archaea (which were abundant at 0 °C). Distance-based redundancy analysis and Procrustes analysis indicated the greater complexity of ecological responses in alpine wetlands, which may be attributed to the higher adaptive capacity of soil microbial communities. Our results suggest that both degradation and warming decrease soil DOM content and microbial activities in alpine wetlands, providing important references for alpine wetland conservation under current climate change.

Seascape genetic study on Laminaria digitata underscores the critical role of sampling schemes

Understanding connectivity patterns exhibited by endangered species living in fragmented habitats is fundamental to improving management and conservation actions. Such improvements can be particularly pressing at the trailing edges of these habitats, where populations are facing the greatest challenges from climate change, and appear even more crucial if the species is commercially harvested. Seascape genetics have been increasingly used to meet these needs. In this study, we examined connectivity patterns among 32 populations of the oarweed kelp Laminaria digitata located at the species’ southern range limit. The distance (or sampling gap) between neighboring populations ranged from a few km to a few 100s of km. By genotyping 11 microsatellite markers, we aimed to (1) refine analyses of population structure; (2) test whether on-shelf islands are genetically more differentiated than mainland populations; (3) evaluate the relative importance of various abiotic conditions in shaping the genetic structure; and (4) evaluate if the relative importance of each environmental factor varied according to sampling schemes. Our analyses revealed a positive relationship between connectivity links and genetic diversity: populations with high levels of connectivity were genetically enriched while isolated populations showed signs of genetic erosion. The genetically impoverished populations corresponded to the southernmost populations as well as populations along the northern coast of Brittany (Locquirec, Saint-Malo Bay) and the northernmost population in Pas-de-Calais. By performing distance-based redundancy analysis on various sampling schemes, geographic distance appeared as the dominant factor influencing connectivity between populations separated by great distances, while hydrodynamic processes were the main factor when analyzing at a final spatial resolution.

O-279 The lower reproductive tract microbiota composition alters upon ovarian stimulation and is associated with, but not accurately predictive of reproductive outcomes following ART

Abstract Study question Are ovarian stimulation (OS) and ART success associated with the microbiota of the lower reproductive tract (LRT), i.e. vagina and cervix? Summary answer Estrogen rise during OS has a pivotal role in the LRT microbiota variation. The LRT microbiota pre-OS, although associated, may not accurately predict ART success. What is known already OS is a key component to enhance success rates in ART. OS triggers a significant rise in serum estrogen levels, which are known to influence the vaginal microbiota. The role of the female LRT microbiota in ART success is increasingly recognized, yet the impact of OS, particularly the estrogen rise, on these microbial communities and how the change may influence ART success remains largely unknown. Additionally, finding putative biomarkers within LRT microbiota could aid in predicting ART success. Understanding this relationship could refine and personalize fertility treatments, but robust evidence is needed to guide microbiota-based clinical decisions in ART. Study design, size, duration Vaginal and cervical swabs were collected longitudinally from patients undergoing ART and this at baseline (pre-OS) and at oocyte retrieval (post-OS). We gathered a final dataset comprising 275 vaginal samples at baseline and 240 samples at oocyte retrieval. Additionally, we defined a prospective cohort of n = 228x2 samples corresponding to patients for which both pre- and post-OS samples were available. The main results as detected within the vaginal samples were confirmed in the cervical samples. Participants/materials, setting, methods Bacterial DNA from −80 °C preserved swabs was extracted in a Tecan Nucleic Acid Extraction Platform, using the QIAamp DNA-Stool-Mini-Kit. Samples for paired-end Illumina MiSeq were constructed using a two-step PCR amplicon approach targeting the V4 region of the 16S rRNA. Then, LotuS, DADA2, the RDP classifier trainset 16 and variance stabilisation (poscounts, DESeq2) were used for read de-multiplexing, pre-processing, taxonomy assignment and transformation, respectively, as recommended for zero-inflated compositional data. Main results and the role of chance First, a confounder analysis revealed that both the menstrual phase and intercourse correlated with the LRT’s baseline microbiota composition (multivariate distance-based redundancy analysis [dbRDA], AdjP&amp;lt;0.05, N = 275). Next, in the paired cohort, we observed that the OS-associated rise in estrogen was correlated with confounder-independent compositional (confounder-adjusted dbRDA, AdjP=0.002, R2=1.14%, N = 228x2) and microbial-feature changes (Wilcoxon test, AdjP&amp;lt;0.05, Ndelta=228) in the LRT. Interestingly, post-OS we noted a decrease in Lactobacillus proportions compared to baseline (in participants sampled at either the follicular or luteal phase of the menstrual cycle). Additionally, post-OS microbiota composition was not associated with the live birth rate (LBR, following the first embryo transfer of the cycle) or the cumulative LBR (CLBR, following all embryo transfers of the cycle), nor with the total number of high-quality (HQ) embryos available (dbRDA, AdjP&amp;gt;0.05, N = 240). Notably, pre-OS microbiota communities and LRT Anaerococcus and Peptoniphilus proportions were associated with (C)LBR (confounder-adjusted dbRDA, AdjP&amp;lt;0.05; Logistic regression, odds-ratio&amp;lt;1, AdjP&amp;lt;0.05, N = 275). Machine learning models determined that vaginal Peptoniphilus and Anaerococcusproportions alone did not have good accuracy/ROC for predicting (C)LBR (test-set;&amp;lt;70%). Notably, the number of HQ embryos showed good accuracy/ROC for CLBR (test-set; 80%/84.5%). Including vaginal Anaerococcus proportions only slightly improved the model’s accuracy/ROC (test-set; 82.5%/85.6%). Limitations, reasons for caution The data’s proportional nature restricted assessing whether the estrogen rise decreased Lactobacillus proportions or increased other bacteria. Luteal phase sampling was avoided given the intravaginal progesterone support. Larger datasets may further improve predictive models. Wider implications of the findings Our study highlights the confounding impact of baseline variables and the influence of the OS-associated estrogen rise on LRT microbiota. It questions the clinical relevance of the LRT microbiota’s impact on reproductive outcomes following ART, warning for caution in microbiota-based decisions in ART. Trial registration number NCT03105453

Non-native flora changes in rural gardens of China: the role of tourism

Human cultivation facilitates the naturalization and subsequent invasion of non-native plant species through, for example, protection from predators or reducing environmental stochasticity. With the development of tourism, non-native plant species have been increasingly introduced into rural home gardens for landscape greening and amenity planting. However, few studies have examined non-native flora in rural home gardens, and in particular the importance of tourism in determining changes of garden non-native flora has not been scrutinized. In this study, we investigated non-native plant species in 135 home gardens across five rural tourism villages in tropical China. Attributes related to garden or household characteristics were also collected through interviews and questionnaires. A distance-based redundancy analysis was then performed to reveal the relationships between the non-native species composition and garden attributes. A total of 338 non-native plant species were recorded in the surveyed gardens. Among them, the majority (63%) were ornamentals, whereas 19% were for nutritional uses and 12% were spontaneous weeds. Gardening preference and distance to tourist attractions governed the non-native compositions, with gardens preferring cultural (ornamental) cultivation or gardens close to tourist attractions having more non-native species. These results highlight an increasing role of tourism in promoting non-native cultivation in rural gardens. Recommendations for species risk assessment, trade and supply regulation, and proper garden management are provided to help harness plant invasion along tourism development in rural China and other regions around the world.

Coastal Dune Vegetation Dynamism and Anthropogenic-Induced Transitions in the Mexican Caribbean during the Last Decade.

In the Mexican Caribbean, environmental changes, hydrometeorological events, and anthropogenic activities promote dynamism in the coastal vegetation cover associated with the dune; however, their pace and magnitude remain uncertain. Using Landsat 7 imagery, spatial and temporal changes in coastal dune vegetation were estimated for the 2011-2020 period in the Sian Ka'an Biosphere Reserve. The SAVI index revealed cover changes at different magnitudes and paces at the biannual, seasonal, and monthly timeframes. Climatic seasons had a significant influence on vegetation cover, with increases in cover during northerlies (SAVI: p = 0.000), while the topographic profile of the dune was relevant for structure. Distance-based multiple regressions and redundancy analysis showed that temperature had a significant effect (p < 0.05) on SAVI patterns, whereas precipitation showed little influence (p > 0.05). The Mann-Kendall tendency test indicated high dynamism in vegetation loss and recovery with no defined patterns, mostly associated with anthropogenic disturbance. High-density vegetation such as mangroves, palm trees, and shrubs was the most drastically affected, although a reduction in bare soil was also recorded. This study demonstrated that hydrometeorological events and climate variability in the long term have little influence on vegetation dynamism. Lastly, it was observed that anthropogenic activities promoted vegetation loss and transitions; however, the latter were also linked to recoveries in areas with pristine environments, relevant for tourism.

One-year effects of stand age, pre-fire treatments, and hillslope aspect on recovery of plant diversity and soil properties in a Mediterranean forest burnt by a severe wildfire

Although several management options are adopted to redirect post-fire forest ecosystems towards less vulnerable and more resilient and functional communities, little is known about the interactions among tree stand age, pre-fire forest management, and slope aspects, and their consequences for plant species and soil properties recovery immediately after severe wildfires. To address this knowledge need, this study evaluates the post-fire changes in species richness and diversity (with a specific focus on regeneration mechanisms and life forms) of regenerating plants as well as the main physico-chemical and biological properties of burned soils with the reciprocal relations. Plant cover and diversity, and many soil properties have been monitored in forests of southeast Spain with mature, middle and young stands, presence of pre-fire treatments or not, and north and south hillslopes about one year after the fire. To this aim, the reciprocal relationships among soil properties and plants were evaluated adopting a combination of statistical techniques (PERMANOVA, Non-metric Multi-Dimensional Scaling, Distance-based Linear Modelling, Distance-based Redundancy Analysis, and Spearman correlation analysis). The damage to soil and vegetation was so high that both plants and pre-fire soil properties slowly recovered. Only a few life forms of vegetation (geophytes and herbaceous chamaephytes) were influenced by the stand age. If combined with soil aspect, stand age resulted in significantly lower germinating species in mature stands and lower resprouters in young stands, both on south hillslopes. Plant diversity was high, and the post-fire regeneration did not change the species richness and evenness. The post-fire changes in soil properties were limited, and only slight small differences in pH and betaglucosidase among stands of different age were found. No evident associations between soil properties and plant diversity were revealed by the low correlation coefficient. The low variance in plant cover and diversity, as well as in soil properties, resulted in a low accuracy of the dbRDA model to reproduce its variability among sites with different pre-fire characteristics.

The effects of climate and soil depth on living and dead bacterial communities along a longitudinal gradient in Chile

Soil bacterial communities play a critical role in shaping soil stability and formation, exhibiting a dynamic interaction with local climate and soil depth. We employed an innovative DNA separation method to characterize microbial assemblages in low-biomass environments such as deserts and distinguish between intracellular DNA (iDNA) and extracellular DNA (eDNA) in soils. This approach, combined with analyses of physicochemical properties and co-occurrence networks, investigated soil bacterial communities across four sites representing diverse climatic gradients (i.e., arid, semi-arid, Mediterranean, and humid) along the Chilean Coastal Cordillera. The separation method yielded a distinctive unimodal pattern in the iDNA pool alpha diversity, increasing from arid to semi-arid climates and decreasing in humid environments, highlighting the rapid feedback of the iDNA community to increasing soil moisture. In the arid region, harsh surface conditions restrict bacterial growth, leading to peak iDNA abundance and diversity occurring in slightly deeper layers than the other sites. Our findings confirmed the association between specialist bacteria and ecosystem-functional traits. We observed transitions from Halomonas and Delftia, resistant to extreme arid environments, to Class AD3 and the genus Bradyrhizobium, associated with plants and organic matter in humid environments. The distance-based redundancy analysis (dbRDA) analysis revealed that soil pH and moisture were the key parameters that influenced bacterial community variation. The eDNA community correlated slightly better with the environment than the iDNA community. Soil depth was found to influence the iDNA community significantly but not the eDNA community, which might be related to depth-related metabolic activity. Our investigation into iDNA communities uncovered deterministic community assembly and distinct co-occurrence modules correlated with unique bacterial taxa, thereby showing connections with sites and key environmental factors. The study additionally revealed the effects of climatic gradients and soil depth on living and dead bacterial communities, emphasizing the need to distinguish between iDNA and eDNA pools.

Taxonomic distinctness and diversity patterns of a polychaete (Annelida) community on the continental shelf of the Southern Gulf of Mexico.

The spatial patterns of taxonomic diversity of annelid polychaete species from the continental shelf in the Southern Gulf of Mexico were examined in this study. We used taxonomic distinctness and its spatial variations to explore the diversity patterns and how they change between Southern Gulf of Mexico regions. In addition, using taxonomic distinctness as a dissimilarity measure and Ward's Clustering, we characterized three distinct faunal assemblages. We also investigated patterns of richness, taxonomic distinctness, and distance decay of similarity between sampling stations as a ß-diversity measure. Finally, we examined the spatial relationships between polychaete assemblages and environmental variables to test the relative importance of spatial and environmental components in annelid polychaete community structure from the Southern Gulf of Mexico. We used a combination of eigenvector-based multivariate analyses (dbMEMs) and distance-based redundancy analysis (dbRDA) to quantify the relative importance of these explanatory variables on the spatial variations of taxonomic distinctness. The significance level of spatial and environmental components to the distribution of polychaete species showed that the combined effect of spatial processes and sediment characteristics explained a higher percentage of the variance than those parameters could alone.

Crop cover and nutrient levels mediate the effects of land management type on aquatic invertebrate richness in prairie potholes.

Aquatic invertebrates provide important ecosystem services, including decomposition and nutrient cycling, and provide nutrition for birds, fish, amphibians, and bats. Thus, the effects of agricultural land management practices on aquatic invertebrates are relevant to farmers, wildlife biologists, and policymakers. Here, we used data on aquatic invertebrates (159 taxa, 73 to species, 75 to genus/family) collected in 40 wetlands in the Canadian prairies to test for direct and indirect relationships among land management types (perennial cover, organic, minimum tillage, conventional), landscape structure (cropland and wetland cover within the surrounding landscape), and water quality (total nutrient levels, turbidity) on species richness of invertebrates using structural equation modelling. Additionally, we assessed variation in community composition within and among wetlands in different land use management types using a direct gradient analysis and variance partitioning. The direct effects of land management type were not supported but we found strong supportive evidence that effects of land management on richness were significantly mediated through cropland cover, nutrient levels, and turbidity. After controlling for these indirect effects, aquatic invertebrate richness decreased along a gradient from the lowest to the highest farming intensity, i.e., richness decreased from perennial cover sites to organic to minimum tillage to conventional sites. Support was also found for negative effects of nutrient levels and turbidity on richness. We did not find significant support for differences in gamma diversity or a simple test (homogeneity of multivariate dispersions) of differences in turnover among land management types; however, land management had a significant effect in distance-based redundancy analysis. Taken together, these results suggest that focusing conservation efforts on reducing cropland erosion and nutrient inputs to wetlands and creating more permanent cover may be effective strategies for conserving richness of aquatic invertebrates in agricultural landscapes in this region.

Seagrass Biodiversity and its Drivers in the Kepulauan Banyak Marine Nature Park, Indonesia

Seagrasses are important marine plants that provide a variety of ecosystem services, including food and shelter for marine life, and protection from coastal erosion. This study investigated the biodiversity (alpha and beta diversity) of seagrass in the Kepulauan Banyak Marine Nature Park, Indonesia, with a specific focus on eight sites. Alpha diversity was calculated using Shannon's index, Simpson's index, and Pielou evenness. Beta diversity was determined using Bray-Curtis dissimilarity and Jaccard dissimilarity allowing us to examine the variations in species composition among different sites. Principal coordinate analysis and Partial distance-based redundancy analysis was used to visualize and investigate the impact of constraint variables to the structure of the seagrass communities. Alpha diversity varied among the sites, with the highest alpha diversity found at the Orongan and Matahari site and the lowest at the Ujung Lolok and Balai sites. The dominant substrate type (mud or sand) was found to be a significant (P≤ 0.01) determinant of seagrass alpha diversity, with mud substrates supporting higher diversity than sand substrates. The relationship between alpha diversity and constrain variables was only significant with closest distance to forest lost and longitude variables. The analysis found that water pH, closest distance to forest lost, mean distance to tourism spots, and closest distance to settlement collectively explained a significant (P≤ 0.001) portion (88.48%) of the variation in beta diversity of seagrass across the sites. The results of this study can be used to develop management strategies for the conservation of seagrass meadows in the park.

Long-Term Benefits of Cenchrus fungigraminus Residual Roots Improved the Quality and Microbial Diversity of Rhizosphere Sandy Soil through Cellulose Degradation in the Ulan Buh Desert, Northwest China.

Long-term plant residue retention can effectively replenish soil quality and fertility. In this study, we collected rhizosphere soil from the residual roots of annual Cenchrus fungigraminus in the Ulan Buh Desert over the past 10 years. The area, depth, and length of these roots decreased over time. The cellulose content of the residual roots was significantly higher in the later 5 years (2018-2022) than the former 5 years (2013-2017), reaching its highest value in 2021. The lignin content of the residual roots did not differ across samples except in 2015 and reached its highest level in 2021. The total sugar of the residual roots in 2022 was 227.88 ± 30.69 mg·g-1, which was significantly higher than that in other years. Compared to the original sandy soil, the soil organic matter and soil microbial biomass carbon (SMBC) contents were 2.17-2.41 times and 31.52-35.58% higher in the later 3 years (2020-2022) and reached the highest values in 2020. The residual roots also significantly enhanced the soil carbon stocks from 2018-2022. Soil dehydrogenase, nitrogenase, and N-acetyl-β-D-glucosidase (S-NAG) were significantly affected from 2019-2022. The rhizosphere soil community richness and diversity of the bacterial and fungal communities significantly decreased with the duration of the residual roots in the sandy soil, and there was a significant difference for 10 years. Streptomyces, Bacillus, and Sphigomonas were the representative bacteria in the residual root rhizosphere soil, while Agaricales and Panaeolus were the enriched fungal genera. The distance-based redundancy analysis and partial least square path model results showed that the duration of residual roots in the sandy soil, S-NAG, and SMBC were the primary environmental characteristics that shaped the microbial community. These insights provide new ideas on how to foster the exploration of the use of annual herbaceous plants for sandy soil improvement in the future.

Correlation between bacterial microbiome and Legionella species in water from public bath facilities by 16S rRNA gene amplicon sequencing.

Public bath facilities are major sources of sporadic cases and outbreaks of Legionella infections. Recently, 16S rRNA gene amplicon sequencing has been used to analyze bacterial characteristics in various water samples from both artificial and natural environments, with a particular focus on Legionella bacterial species. However, the relationship between the bacterial community and Legionella species in the water from public bath facilities remains unclear. In terms of hygiene management, it is important to reduce the growth of Legionella species by disinfecting the water in public bath facilities. Our findings contribute to the establishment of appropriate hygiene management practices and provide a basis for understanding the potential health effects of using bath and shower water available in public bath facilities.

Temporal dynamics of the ichthyoplankton assemblages in the central Aegean Sea during one year and the effects of ecological factors

In this investigation, vertical and horizontal sampling was performed monthly, covering a year, from 16 stations situated in Sığacık Bay. In ichthyoplankton sampling, a standard-type plankton net with a 350-micron mesh size for vertical sampling and a 500-micron mesh size for horizontal sampling was used. This study aimed to investigate temporal changes in the ichthyoplankton assemblages in Sığacık Bay and their relationship with ecological factors. A total of 113 fish taxa belonging to 42 families were identified. The Sparidae, Engraulidae, and Labridae families were found to be the most dominant among the eggs and larvae, with Engraulis encrasicolus, Coris julis, Mullus barbatus, and Gobius niger being the most prevalent species. The highest biodiversity index values were observed in April and May. The cluster analysis revealed the existence of three distinct groups.Based on the SIMPER analysis, S. aurata emerges as the indicator species for months characterised by lower water temperatures, G. niger stands as the indicator species for warm months, and E. encrasicolus represents the indicator species for the hottest months group. Both distance-based linear modelling (DistLM) and distance-based redundancy analysis (dbRDA) highlighted that water temperature, salinity, and chlorophyll-a were the main variables that influenced the temporal variation of the ichthyoplankton assemblage. The results of this study will be of great significance in comprehending the responses of the ichthyoplankton assemblages residing in analogous ecosystems to ecological variables.

Drivers of desert plant beta diversity on the Qinghai-Tibet plateau.

The desert ecosystem of the Qinghai-Tibet Plateau (QTP) is an important component of China's desert ecosystem. Studying the mechanisms shaping the taxonomic, phylogenetic, and functional beta diversity of plant communities in the QTP desert will help us to promote scientific conservation and management of the region's biodiversity. This study investigated the effects of environmental (including altitude, climate factors, and soil factors) and geographic distances on three facets of beta diversity as well as their turnover and nestedness components based on field survey data. The results showed that turnover components dominate the three facets of beta diversity. However, the turnover contributions to phylogenetic and functional beta diversity were lower than for taxonomic beta diversity. Environmental distance had a greater influence than geographic distance, with the former uniquely explaining 15.2%-22.8% of beta diversity and the latter explaining only 1.7%-2.4%. Additionally, the explanatory power of different factors for beta diversity differed between herbs and shrubs, with environmental distance being more important for the latter. Distance-based redundancy analysis suggested that soil total potassium content had a substantial impact on the beta diversity of three dimensions, with mean temperature of the coldest month and soil total phosphorus content having a substantial impact on taxonomic and functional beta diversity as well. Our results support that environmental sorting plays a predominant role in shaping plant community composition across QTP desert ecosystems. To maintain the plant diversity of this region, it is crucial to prioritize the conservation of its diverse environmental conditions and actively mitigate its degradation by anthropogenic pressures.

The Changes in Soil Microbial Communities and Assembly Processes along Vegetation Succession in a Subtropical Forest

Soil microbes are the primary drivers of the material cycling of the forest ecosystem, and understanding how microbial structure and composition change across succession assists in clarifying the mechanisms behind succession dynamics. However, the response of soil microbial communities and assembly processes to succession is poorly understood in subtropical forests. Thus, through the “space instead of time” and high throughput sequencing method, the dynamics of the soil bacterial and fungal communities and assembly process along the succession were studied, where five succession stages, including Abandoned lands (AL), Deciduous broad-leaved forests (DB), Coniferous forests (CF), Coniferous broad-leaved mixed forests (CB), and Evergreen broad-leaved forests (EB), were selected in a subtropical forest on the western slope of Wuyi Mountain, southern China. The results demonstrated that succession significantly decreased soil bacterial α-diversity but had little effect on fungal α-diversity. The composition of soil bacterial and fungal communities shifted along with the succession stages. LEfSe analysis showed the transition from initial succession microbial communities dominated by Firmicutes, Bacteroidota, Ascomycota, and Chytridiomycota to terminal succession communities dominated by Actinobacteriota and Basidiomycota. Distance-based redundancy analysis (db-RDA) revealed that soil total organic carbon (TOC) was the main factor explaining variability in the structure of soil bacterial communities, and multiple soil environmental factors such as the TOC, soil total nitrogen (TN), C:N ratio, and pH co-regulated the structure of fungi. The null models illustrated that deterministic processes were dominant in the soil bacterial communities, while the stochastic processes contributed significantly to the soil fungal communities during succession. Collectively, our results suggest that different patterns are displayed by the soil bacterial and fungal communities during the succession. These findings enhance our comprehension of the processes that drive the formation and maintenance of soil microbial diversity throughout forest succession.

Calorie restriction during gestation impacts maternal and offspring fecal microbiome in mice.

Maternal undernutrition is the most common cause of fetal growth restriction (FGR) worldwide. FGR increases morbidity and mortality during infancy, as well as contributes to adult-onset diseases including obesity and type 2 diabetes. The role of the maternal or offspring microbiome in growth outcomes following FGR is not well understood. FGR was induced by 30% maternal calorie restriction (CR) during the second half of gestation in C57BL/6 mice. Pup weights were obtained on day of life 0, 1, and 7 and ages 3, 4 and 16 weeks. Fecal pellets were collected from pregnant dams at gestational day 18.5 and from offspring at ages 3 and 4 weeks of age. Bacterial genomic DNA was used for amplification of the V4 variable region of the 16S rRNA gene. Multivariable associations between maternal CR and taxonomic abundance were assessed using the MaAsLin2 package. Associations between microbial taxa and offspring outcomes were performed using distance-based redundancy analysis and Pearson correlations. FGR pups weighed about 20% less than controls. Beta but not alpha diversity differed between control and CR dam microbiomes. CR dams had lower relative abundance of Turicibacter, Flexispira, and Rikenella, and increased relative abundance of Parabacteroides and Prevotella. Control and FGR offspring microbiota differed by beta diversity at ages 3 and 4 weeks. At 3 weeks, FGR offspring had decreased relative abundance of Akkermansia and Sutterella and increased relative abundance of Anaerostipes and Paraprevotella. At 4 weeks, FGR animals had decreased relative abundance of Allobaculum, Sutterella, Bifidobacterium, and Lactobacillus, among others, and increased relative abundance of Turcibacter, Dorea, and Roseburia. Maternal Helicobacter abundance was positively associated with offspring weight. Akkermansia abundance at age 3 and 4 weeks was negatively associated with adult weight. We demonstrate gut microbial dysbiosis in pregnant dams and offspring at two timepoints following maternal calorie restriction. Additional research is needed to test for functional roles of the microbiome in offspring growth outcomes.