Mantel Test Research Articles

The dependent correlation between soil multifunctionality and bacterial community across different farmland soils.

Microorganisms play a critical role in soil biogeochemical cycles, but it is still debated whether they influence soil biogeochemical processes through community composition and diversity or not. This study aims to investigate variation in bacterial community structure across different soils and its correlation to soil multifunctionality. Soil samples were collected from five typical farmland zones along distinct climatic gradients in China. The high-throughput sequencing (Illumina MiSeq) of 16S rRNA genes was employed to analyze bacterial community composition in each soil sample. Multivariate analysis was used to determine the difference in soil properties, microbial community and functioning, and their interactions. Cluster and discrimination analysis indicated that bacterial community composition was similar in five tested soil samples, but bacterial richness combined with soil enzyme activities and potential nitrification rate (PNR) contributed most to the differentiations of soil samples. Mantel test analysis revealed that bacterial community composition and richness were more significantly shaped by soil nutrient conditions and edaphic variables than bacterial diversity. As for soil multifunctionality, soil microbial community level physiological profiles were little affected by abiotic and biotic factors, while soil enzymes and PNR were also significantly related to bacterial community composition and richness, in addition to soil N and P availability. Cumulatively, soil enzymes' activities and PNR were greatly dependent on bacterial community composition and richness not diversity, which in turn were greatly modified by soil N and P availability. Therefore, in the future it should be considered for the role of fertilization in the modification of bacterial community and the consequent control of nutrient cycling in soil.

Soil depth and geographic distance modulate bacterial β-diversity in deep soil profiles throughout the U.S. Corn Belt.

Understanding how microbial communities are shaped across spatial dimensions is of fundamental importance in microbial ecology. However, most studies on soil biogeography have focused on the topsoil microbiome, while the factors driving the subsoil microbiome distribution are largely unknown. Here we used 16S rRNA amplicon sequencing to analyse the factors underlying the bacterial β-diversity along vertical (0-240 cm of soil depth) and horizontal spatial dimensions (~500,000 km2 ) in the U.S. Corn Belt. With these data we tested whether the horizontal or vertical spatial variation had stronger impacts on the taxonomic (Bray-Curtis) and phylogenetic (weighted Unifrac) β-diversity. Additionally, we assessed whether the distance-decay (horizontal dimension) was greater in the topsoil (0-30 cm) or subsoil (in each 30 cm layer from 30-240 cm) using Mantel tests. The influence of geographic distance versus edaphic variables on the bacterial communities from the different soil layers was also compared. Results indicated that the phylogenetic β-diversity was impacted more by soil depth, while the taxonomic β-diversity changed more between geographic locations. The distance-decay was lower in the topsoil than in all subsoil layers analysed. Moreover, some subsoil layers were influenced more by geographic distance than any edaphic variable, including pH. Although different factors affected the topsoil and subsoil biogeography, niche-based models explained the community assembly of all soil layers. This comprehensive study contributed to elucidating important aspects of soil bacterial biogeography including the major impact of soil depth on the phylogenetic β-diversity, and the greater influence of geographic distance on subsoil than on topsoil bacterial communities in agroecosystems.

The first Brazilian bovine breed: structure and genetic diversity of the Curraleiro Pé-duro.

The production of animal-based foods from native breeds have a synergistic relationship with the regional culture, the local climate, and mainly the maintenance of alternative genetic resources for a system with a lower environmental impact. Thus the efficiency of conservation and production depends on assessing the variability of these local breeds. In the case of Curraleiro Pé-duro cattle, the most adapted individuals have undergone natural selection over five hundred years in the Brazilian savannas, mating with little or no human interference. The peculiarities of these biomes, where the regional flora is the food base and cattle is raised in extensive areas, likely influenced the genetic composition of the different groups that make up the first cattle breed of Brazil. To evaluate the composition, diversity, variation, differentiation, and genetic structure of the populations studied, samples of hair follicles from 474 individuals of different animal categories (calves, yearlings, heifers, cows, and bulls) from three farms, defined as subpopulations "A", "B", and "C", were collected. The animals were genotyped for 17 microsatellite markers using a DNA sequencer. After verification of monomorphic alleles, alleles outside the expected size range, and for the presence of stutter bands, the results were subjected to statistical analysis. The markers used were suitable for the proposed application with a mean Polymorphism Information Content (PIC) of 0.62. On average, the effective alleles were 4.25 per marker, with mean heterozygosities of 0.74 (observed and expected), which was lower in herd A (0.70) in comparison to herds B (0.77) and C (0.74). The analysis of molecular variance (AMOVA) revealed a higher rate of variation within herds (98.5%) and lower among herds (1.5%) (FSTranging from 0.00723 and 0.03198; p-values < 0.05). However no significant differences among herds where found with the Mantel test based on geographic distances. The formation of genetic clusters of all animals sampled with the software Structure resulted in minimum cluster values, with two main genetic groups (K=2) observed among the evaluated animals. Therefore, based on PIC and heterozygosity values, a wide genetic diversity was observed, despite little differences in population structure (AMOVA, FST, and Structure results) among sampling sites.

Integrated Microbiome and Metabolomic Analysis Reveal Responses of Rhizosphere Bacterial Communities and Root exudate Composition to Drought and Genotype in Rice (Oryza sativa L.)

BackgroundAs climate change events become more frequent, drought is an increasing threat to agricultural production and food security. Crop rhizosphere microbiome and root exudates are critical regulators for drought adaptation, yet our understanding on the rhizosphere bacterial communities and root exudate composition as affected by drought stress is far from complete. In this study, we performed 16S rRNA gene amplicon sequencing and widely targeted metabolomic analysis of rhizosphere soil and root exudates from two contrasting rice genotypes (Nipponbare and Luodao 998) exposed to drought stress.ResultsA reduction in plant phenotypes was observed under drought, and the inhibition was greater for roots than for shoots. Additionally, drought exerted a negligible effect on the alpha diversity of rhizosphere bacterial communities, but obviously altered their composition. In particular, drought led to a significant enrichment of Actinobacteria but a decrease in Firmicutes. We also found that abscisic acid in root exudates was clearly higher under drought, whereas lower jasmonic acid and L-cystine concentrations. As for plant genotypes, variations in plant traits of the drought-tolerant genotype Luodao 998 after drought were smaller than those of Nipponbare. Interestingly, drought triggered an increase in Bacillus, as well as an upregulation of most organic acids and a downregulation of all amino acids in Luodao 998. Notably, both Procrustes analysis and Mantel test demonstrated that rhizosphere microbiome and root exudate metabolomic profiles were highly correlated. A number of differentially abundant genera responded to drought and genotype, including Streptomyces, Bacillus and some members of Actinobacteria, were significantly associated with organic acid and amino acid contents in root exudates. Further soil incubation experiments showed that Streptomyces was regulated by abscisic acid and jasmonic acid under drought.ConclusionsOur results reveal that both drought and genotype drive changes in the compositions of rice rhizosphere bacterial communities and root exudates under the greenhouse condition, and that organic acid exudation and suppression of amino acid exudation to select specific rhizosphere bacterial communities may be an important strategy for rice to cope with drought. These findings have important implications for improving the adaptability of rice to drought from the perspective of plant–microbe interactions.

Environmental predictors affect α- and β-diversity of tropical bromeliad macroinvertebrates

We tested the hypothesis that abiotic predictors, both influence α and β-diversity of macroinvertebrate communities in the phytotelmata of the terrestrial bromeliad, Vriesea philippocoburgii. Macroinvertebrates were sampled in 58 bromeliads in a restinga in Brazil and estimated both the α and β-diversity in each bromeliad, and then partitioning them into nestedness and turnover. We then used Generalized Linear Models and partial Mantel tests to identify which environmental factors predict these diversity components for the macroinvertebrate communities. The size of the plant positively influenced α-diversity, whereas light intensity strongly influenced β-diversity. Both components were influenced by organic matter. Plants exhibiting large differences in values of organic matter and light intensity had different macroinvertebrate communities. Furthermore, bromeliad systems exhibit high β-diversity values governed by turnover. Our findings demonstrate the importance of considering α and β-diversities in studies that assess the diversity patterns of aquatic macroinvertebrates and suggest that environmental changes that modify the structure of aquatic macroinvertebrate communities could have impacts on ecosystem processes.

SSR and SNP Marker-Based Investigation of Indian Rice Landraces in Relation to Their Genetic Diversity, Population Structure, and Geographical Isolation

India is blessed with an abundance of diverse rice landraces in its traditional cultivated areas. Two marker systems (simple sequence repeats (SSR) and single nucleotide polymorphism (SNP)) were used to study a set of 298 rice landrace accessions collected from six different regions of India (Andaman and Nicobar Islands, Chhattisgarh, Jharkhand, Uttar Pradesh, Uttarakhand, and West Bengal). Thirty hyper-variable simple sequence repeats (HvSSRs) and 32,782 single nucleotide polymorphisms (SNPs) were used in inferring genetic structure and geographical isolation. Rice landraces from Uttar Pradesh were the most diverse, with a gene diversity value of 0.42 and 0.49 with SSR and SNP markers, respectively. Neighbor-joining trees classified the rice landraces into two major groups with SSR and SNP markers, and complete geographical isolation was observed with SSR markers. Fast STRUCTURE analysis revealed four populations for SSR markers and three populations for SNP markers. The population structure with SSR markers showed that few individuals from Uttarakhand and Andaman and Nicobar Islands were grouped in small clusters. Population structure analysis with SNP markers showed not very distinct region-wise clustering among the rice landraces. Discriminant analysis of principal components (DAPC) and minimum spanning network (MSN) using SSR markers showed region-wise grouping of landraces with some intermixing, but DAPC and MSN with SNP markers showed very clear region-wise clustering. Genetic differentiation of rice landraces between the regions was significant with both SSR (Fst 0.094–0.487) and SNP markers (Fst 0.047–0.285). A Mantel test revealed a positive correlation between the genetic and geographic distance of rice landraces. The present study concludes that rice landraces investigated in this study were very diverse, and unlinked SSR markers show better geographical isolation than a large set of SNP markers.

Fine-Scale Spatial Genetic Structure of Remnant Populations of Abies religiosa, in a Temperate Forest in Central Mexico

Genetic structure of a population can be molded by the resistance of the landscape or the distance between populations that function as barriers to gene flow. We analyzed the population genetic structure of Abies religiosa on a fine spatial scale and examined isolation models by resistance and distance. We collected vegetative tissue from populations located at the altitudinal extremes of the distribution range of the species on three slopes of La Malinche National Park (LMNP) (South, North, and East) in central Mexico. Genomic DNA was obtained using the CTAB 2X method, and eight microsatellite chloroplast loci were amplified. The genetic structure was identified based on an Analysis of Molecular Variance, a Discriminant Analysis of Principal Components with cross-validation and a spatial Principal Component Analysis using the Gabriel-type connectivity network. The isolation hypotheses were evaluated by constructing partial Mantel tests using Reciprocal Causal Modeling and Maximum Likelihood Population Effects models. A genetic structure of isolation by resistance to elevation was identified, and two genetic groups were recognized: one including populations of the South slope and the other comprising populations of the North and East slopes. We detected in Abies religiosa populations of the LMNP an isolation by resistance to elevation that determines the genetic structure, and the greatest genetic exchange between groups of populations located at higher altitudes. It is suggested to promote the connectivity between slopes through assisted migration and immediately halt land-use changes, as part of the actions to preserve genetic diversity in the LMPN. This study contributes to the knowledge of the spatial genetic structure of species at risk in the Mexican temperate forest for their conservation.

Convergence in floodplain pond communities indicates different pathways to community assembly

Disturbance can strongly influence ecosystems, yet much remains unknown about the relative importance of key processes (selection, drift, and dispersal) in the recovery of ecological communities following disturbance. We combined field surveys with a field experiment to elucidate mechanisms governing the recovery of aquatic macroinvertebrates in habitats of an alluvial floodplain following flood disturbance. We monitored macroinvertebrates in 24 natural parafluvial habitats over 60 days after a major flood, as well as the colonization of 24 newly-built ponds by macroinvertebrates over 45 days in the same floodplain. We examined the sources of environmental variation and their relative effects on aquatic assemblages using a combination of null models and Mantel tests. We also used a joint species distribution model to investigate the importance of primary metacommunity structuring processes during recovery: selection, dispersal, and drift. Contrary to expectations, we found that beta diversity actually decreased among natural habitats over time after the flood or the creation of the ponds, instead of increasing. This result was despite environmental predictors showing contrasting patterns for explaining community variation over time in the natural habitats compared with the experimental ponds. Flood heterogeneity across the floodplain and spatial scale differences between the experimental ponds and the natural habitats seemingly constrained the balance between deterministic and stochastic processes driving the ecological convergence of assemblages over time. While environmental selection was the dominant structuring process in both groups, biotic interactions also had a prominent influence on community assembly. These findings have profound implications towards understanding metacommunity structuring in riverscapes that includes common linkages between disturbance heterogeneity, spatial scale properties, and community composition.

Uncovering Patterns and Relationships: A Multivariate Data Analysis Case Study

To distinguish between different cheese varieties, a total of 24 commercial cheeses were examined using three distinct methods to assess both general and thermophysical parameters. Rheological properties of different temperatures, stretch ability, melt ability and the formation of free oil were already present in the data. Box plots helped classifying textures of different cheese types on the basis of the general and thermophysical properties. Cluster analysis and multidimensional scaling helped classify the cheese types based on a variety of properties. Principal component analysis was applied, too, to the data set to receive a mapping of the cheese. A reduction of the analyzed parameters to three principal components accounting for 76.3% of the total variation was achieved, indicating that the methods are well suited to characterize the cheese samples. Mapping aids cheese producers to design new products with defined characteristics by affecting the manufacturing protocol. Also it helps cheese dealers to decide whether to buy a new variety of cheese produced in the market. Key Words: Multivariate data, Andrew’s curves, cluster analysis, mantel test, multidimensional scaling, principal component analysis, general properties, thermophysical properties of cheese, R programming.

Genetic variation of species Tacca chantrieri in northern Vietnam using ISSR markers for conservation purposes

Tacca chantrieri is a useful medicinal plant native to lowland tropical forests in northern Vietnam. However, it is threatened with extinction owing to habitat fragmentation and overexploitation. Genetic diversity in 5 natural populations of T. chantrieri was examined using 20 ISSR primers polymorphism. Our study showed that average PIC was 0.253 (0.018 - 0.460) and average PPB was 62.49 % (40- 85.71). 5 populations had modest genetic variability (Na = 1.384, Ne = 1.32, Ho = 0.182, He = 0.178 and I = 0.258) and the species level had a low value (Na = 1.892, Ne = 1.744, Ho = 0.293, He = 0.389 and I = 0.549). The lowest levels of genetic diversity were detected in Cuc Phuong population (Na = 1.135, Ne = 1.021, Ho = 0.091, He = 0.078 and I = 0.116) and the highest levels were detected in Ba Vi population (Na = 1.555, Ne = 1.436, Ho = 0.247, He = 0.242 and I = 0.350). A substantial positive connection between genetic distance and geographic distance was discovered using the Mantel test (R2 = 0.5086). The implications of the results of this study to conserve the genetic resources of T. chantrieri were discussed.

Integrating bulk and single-cell RNA sequencing data reveals the relationship between intratumor microbiome signature and host metabolic heterogeneity in breast cancer.

Nowadays, it has been recognized that gut microbiome can indirectly modulate cancer susceptibility or progression. However, whether intratumor microbes are parasitic, symbiotic, or merely bystanders in breast cancer is not fully understood. Microbial metabolite plays a pivotal role in the interaction of host and microbe via regulating mitochondrial and other metabolic pathways. And the relationship between tumor-resident microbiota and cancer metabolism remains an open question. 1085 breast cancer patients with normalized intratumor microbial abundance data and 32 single-cell RNA sequencing samples were retrieved from public datasets. We used the gene set variation analysis to evaluate the various metabolic activities of breast cancer samples. Furthermore, we applied Scissor method to identify microbe-associated cell subpopulations from single-cell data. Then, we conducted comprehensive bioinformatic analyses to explore the association between host and microbe in breast cancer. Here, we found that the metabolic status of breast cancer cells was highly plastic, and some microbial genera were significantly correlated with cancer metabolic activity. We identified two distinct clusters based on microbial abundance and tumor metabolism data. And dysregulation of the metabolic pathway was observed among different cell types. Metabolism-related microbial scores were calculated to predict overall survival in patients with breast cancer. Furthermore, the microbial abundance of the specific genus was associated with gene mutation due to possible microbe-mediated mutagenesis. The infiltrating immune cell compositions, including regulatory T cells and activated NK cells, were significantly associated with the metabolism-related intratumor microbes, as indicated in the Mantel test analysis. Moreover, the mammary metabolism-related microbes were related to T cell exclusion and response to immunotherapy. Overall, the exploratory study shed light on the potential role of the metabolism-related microbiome in breast cancer patients. And the novel treatment will be realized by further investigating the metabolic disturbance in host and intratumor microbial cells.

Genetic variation of arta populations ( Calligonum polygonoides subsp. comosum) in Egypt: Genepools for biodiversity and afforestation

Genetic diversity manipulates a prime and vital role in the sustainable use of genetic resources. The data highlighted more insights into the genetic diversity of the arta plant ( Calligonum polygonoides subsp. comosum) populations collected from three localities, Qalabshu ( QQ), Mutubas ( MM) and Gamasa (GG), in Egypt as gene pool for biodiversity conservation and afforestation. Random amplified polymorphic DNA (RAPD) markers investigated the population pattern and structure. A total of 129-amplicons oscillated from 145 to 1505 bp and a total of 19-amplicons were specific markers with an average of nine bands for each population. The Shannon index (I) scored at an average of 0.3. The diversity ( h) oscillated from 0.11 to 0.25. The similarity matrices based on Jaccard coefficient recorded positive values. A higher correlation (r = 0.83) was between the combined Qalabshu (QQ) and Mutubas (MM) matrices using the Mantel test with 1,000 permutations. This species has higher adaptability for their regions. This gene pool is a valuable reservoir for enriching genetic diversity and provides basal information for the biodiversity conservation of a dominant species. The dominant species can be utilised in afforestation in the same region or another region which has the same environmental conditions.

Population genetic characteristics of Aedes aegypti in 2019 and 2020 under the distinct circumstances of dengue outbreak and the COVID-19 pandemic in Yunnan Province, China.

Introduction: Since Aedes aegypti invaded Yunnan Province in 2002, its total population has continued to expand. Shi et al. used microsatellite and mitochondrial molecular markers to study the Ae. aegypti populations in Yunnan Province in 2015 and 2016, found that it showed high genetic diversity and genetic structure. However, there are few studies on the population genetic characteristics of Ae. aegypti in Yunnan Province under different levels of human intervention. This study mainly used two common types of molecular markers to analyze the genetic characteristics of Ae. aegypti, revealing the influence of different input, prevention and control pressures on the genetic diversity and structure of this species. Understanding the genetic characteristics of Ae. aegypti populations and clarifying the diversity, spread status, and source of invasion are essential for the prevention, control and elimination of this disease vector. Methods: We analyzed the genetic diversity and genetic structure of 22 populations sampled in Yunnan Province in 2019 and 17 populations sampled in 2020 through nine microsatellite loci and COI and ND4 fragments of mitochondrial DNA. In 2019, a total of 22 natural populations were obtained, each containing 30 samples, a total of 660 samples. In 2020, a total of 17 natural populations were obtained. Similarly, each population had 30 samples, and a total of 510 samples were obtained. Results: Analysis of Ae. aegypti populations in 2019 and 2020 based on microsatellite markers revealed 67 and 72 alleles, respectively. The average allelic richness of the populations in 2019 was 3.659, while that in 2020 was 3.965. The HWE analysis of the 22 populations sampled in 2019 revealed significant departure only in the QSH-2 population. The 17 populations sampled in 2020 were all in HWE. The average polymorphic information content (PIC) values were 0.546 and 0.545, respectively, showing high polymorphism. The average observed heterozygosity of the 2019 and 2020 populations was 0.538 and 0.514, respectively, and the expected average heterozygosity was 0.517 and 0.519, showing high genetic diversity in all mosquito populations. By analyzing the COI and ND4 fragments in the mitochondrial DNA of Ae. aegypti, the populations sampled in 2019 had a total of 10 COI haplotypes and 17 ND4 haplotypes. A total of 20 COI haplotypes were found in the populations sampled in 2020, and a total of 24 ND4 haplotypes were obtained. STRUCTURE, UPGMA and DAPC cluster analyses and a network diagram constructed based on COI and ND4 fragments showed that the populations of Ae. aegypti in Yunnan Province sampled in 2019 and 2020 could be divided into two clusters. At the beginning of 2020, due to the impact of COVID-19, the flow of goods between the port areas of Yunnan Province and neighboring countries was reduced, and the sterilization was more effective when goods enter the customs, leading to different immigration pressures on Ae. aegypti population in Yunnan Province between 2019 and 2020, the source populations of the 2019 and 2020 populations changed. Mantel test is generally used to detect the correlation between genetic distance and geographical distance, the analysis indicated that population geographic distance and genetic distance had a moderately significant correlation in 2019 and 2020 (2019: p < 0.05 R2 = 0.4807, 2020: p < 0.05 R2 = 0.4233). Conclusion: Ae. aegypti in Yunnan Province maintains a high degree of genetic diversity. Human interference is one reason for the changes in the genetic characteristics of this disease vector.

Biotic interactions contribute more than environmental factors and geographic distance to biogeographic patterns of soil prokaryotic and fungal communities.

Recent studies have shown distinct soil microbial assembly patterns across taxonomic types, habitat types and regions, but little is known about which factors play a dominant role in soil microbial communities. To bridge this gap, we compared the differences in microbial diversity and community composition across two taxonomic types (prokaryotes and fungi), two habitat types (Artemisia and Poaceae) and three geographic regions in the arid ecosystem of northwest China. To determine the main driving factors shaping the prokaryotic and fungal community assembly, we carried out diverse analyses including null model, partial mantel test and variance partitioning analysis etc. The findings suggested that the processes of community assembly were more diverse among taxonomic categories in comparison to habitats or geographical regions. The predominant driving factor of soil microbial community assembly in arid ecosystem was biotic interactions between microorganisms, followed by environmental filtering and dispersal limitation. Network vertex, positive cohesion and negative cohesion showed the most significant correlations with prokaryotic and fungal diversity and community dissimilarity. Salinity was the major environmental variable structuring the prokaryotic community. Although prokaryotic and fungal communities were jointly regulated by the three factors, the effects of biotic interactions and environmental variables (both are deterministic processes) on the community structure of prokaryotes were stronger than that of fungi. The null model revealed that prokaryotic community assembly was more deterministic, whereas fungal community assembly was structured by stochastic processes. Taken together, these findings unravel the predominant drivers governing microbial community assembly across taxonomic types, habitat types and geographic regions and highlight the impacts of biotic interactions on disentangling soil microbial assembly mechanisms.

Strengthening in microbiota dynamics and C, N, S transformation induced by novel synthesized pyrite/PHBV composites for advanced nitrogen and phosphate removal: Overlooked sulfate reduction process

Fine-grained pyrites are difficult to be denitrified under natural environment due to chemical oxidation with O2. In this study, the pyrite/PHBV composites were synthesized through high-temperature melting and realized nitrogen and phosphate removal under natural aerobic conditions. Results showed that pyrite/PHBV-40 composites had the highest denitrification rate of 0.61 mg NO3−–N /(L·h) with low SO42− production, and its removal efficiency of nitrogen and phosphorus was 98% and 41%, respectively. Microbial community structure analysis revealed that the enrich sulfate-reducing bacteria (SRB) on the pyrite/PHBV-40 composites demonstrated that the sulfate reduction driven by SRB enhanced denitrification process, and thereby the S cycle could underpin the potential self-sustainability of pyrite/PHBV-40 composites. Co-occurrence network analysis showed that Fe oxidizers/reducers (e.g., Ferruginibacter/Geobacter) and SRB (e.g., Desulfovibrio) were the keystone species in microbial community. Bugbase analysis showed that formed biofilms mainly consisted of aerobic and facultative anaerobic strains, which was corresponding to structure of biofilm including aerobic and anoxic layer. Partial mantel test revealed the total Fe and nutrients (e.g., N and P) are the drivers in OTU and phenotype composition, respectively. Metabolic pathway analysis suggested that pyrite/PHBV composites may not only accelerate glycolysis with rapid hydrolysis of PHBV, but also enhance the TCA cycle with high production of ATP and NADH. The final product of nitrate reduction is N2O or NO, and the cysJ gene play an important role in sulfate reduction in pyrite/PHBV systems. Overall, the novel synthesized pyrite/PHBV composites are an ideal functional material with high denitrification rate, no secondary pollution and long service life. Our study highlights pyrite/PHBV-induced strength in microbiota dynamics and C, N, S transformation, therein, the sulfate reduction process cannot be overlooked.

Dispersal syndromes mediate phylogenetic distance decay relationships in a dendritic stream network

AbstractAimUnderstanding the mechanisms underlying the structure and connectivity of ecological communities is a central issue in biogeography. Dispersal syndromes are tightly woven into organisms' life history seen across populations and communities, but measuring dispersal is still complicated in practice. We investigated the role of dispersal syndromes (here, associated with body size, adult flying ability and voltinism) to predict phylogenetic distance decay relationships (DDRs) of aquatic insect assemblages in dendritic stream networks.LocationDu River Basin, China.TaxonAquatic insects (Coleoptera, Diptera, Ephemeroptera, Hemiptera, Lepidoptera, Megaloptera, Odonata, Plecoptera and Trichoptera).MethodsWe applied multiple methods (i.e. deconstruction approach, null models, Mantel tests and partial Mantel tests) to enhance our basic understanding of phylogenetic distance decay patterns. To provide additional insights into correlates of phylogenetic dissimilarity between stream sites, we modelled potential dispersal routes based on overland, watercourse and cost distances.ResultsOverland distances were among the main correlates of phylogenetic distance decay in the stream networks studied, suggesting that aquatic insects disperse overland seeking for habitats suitable for survival and reproduction. However, local environmental filtering was generally more important for phylogenetic DDRs than geographical distances alone. The interaction between environmental vs. dispersal processes in driving spatial patterns of phylogenetic dissimilarity was contingent on different dispersal syndromes. More specifically, significant phylogenetic DDRs were detected only for subsets of large‐bodied, univoltine taxa with strong adult flying abilities, such as dragonflies.Main ConclusionsOverall, historical constraints affect the phylogenetic DDRs in aquatic insects. Dispersal syndromes associated with body size, adult flying ability and voltinism are key features underlying distance decay in phylogenetic assemblage similarity and the evolutionary legacies of aquatic insects in dendritic stream networks.

Genetic Diversity and Population Structure Analysis in the Chinese Endemic Species Michelia crassipes Based on SSR Markers

Michelia crassipes Y. W. Law (Magnoliaceae) is endemic to China and is the only species with purple flowers in the genus Michelia. It is commonly used as an important parent for flower color improvement and hybrid breeding. M. crassipes is recognized as an endangered plant. An urgent need exists to explore the genetic diversity of M. crassipes to efficiently select hybrid parents and develop efficient conservation strategies. In this study, a total of 128 samples were selected from seven natural populations of M. crassipes to explore their genetic diversity and structure. A total of 14 microsatellite (SSR) markers with high polymorphism and repeatability were developed, and 218 alleles were detected. This study mainly revealed three results: (1) The parameters of expected heterozygosity (He = 0.536) and mean Shannon’s information index (I = 1.121) revealed moderately high levels of genetic diversity for the M. crassipes natural population; (2) The genetic differentiation coefficient (Fst = 0.108) showed that there was a low level of genetic differentiation, and AMOVA indicated that genetic variation existed mainly within populations and that there was frequent gene exchange between populations; and (3) The population genetic structure analysis showed that seven natural populations originated from two ancestral groups, and the Mantel test revealed that genetic and geographical distances between populations were significantly correlated. Our study is the first to explore the genetic diversity and structure of the M. crassipes natural population, which provides an important reference for the collection, conservation and utilization of Michelia crassipes germplasm resources.

Multi-omics approach to study the dual effects of novel proteins on the intestinal health of juvenile largemouth bass (Micropterus salmoides) under an alternate feeding strategy.

In an effort to minimize the usage of fishmeal in aquaculture, novel protein diets, including Tenebrio molitor, cottonseed protein concentrate, Clostridium autoethanogenum, and Chlorella vulgaris were evaluated for their potential to replace fishmeal. Nevertheless, comprehensive examinations on the gut health of aquatic animals under an alternate feeding strategy when fed novel protein diets are vacant. Five isonitrogenous and isolipidic diets containing various proteins were manufactured, with a diet consisting of whole fishmeal serving as the control and diets containing novel proteins serving as the experimental diets. Largemouth bass (Micropterus salmoides) with an initial body weight of 4.73 ± 0.04g employed as an experimental animal and given these five diets for the first 29 days followed by a fishmeal diet for the next 29 days. The results of this study demonstrated that the growth performance of novel protein diets in the second stage was better than in the first stage, even though only the C. vulgaris diet increased antioxidant capacity and the cottonseed protein concentrate diet decreased it. Concerning the intestinal barriers, the C. autoethanogenum diet lowered intestinal permeability and plasma IL-1β/TNF-α. In addition, the contents of intestinal immunological factors, namely LYS and sIgA-like, were greater in C. vulgaris than in fishmeal. From the data analysis of microbiome and metabolome, the levels of short chain fatty acids (SCFAs), anaerobic bacteria, Lactococcus, and Firmicutes were significantly higher in the C. autoethanogenum diet than in the whole fishmeal diet, while the abundance of Pseudomonas, aerobic bacteria, Streptococcus, and Proteobacteria was lowest. However, no extremely large differences in microbiota or short chain fatty acids were observed between the other novel protein diets and the whole fishmeal diet. In addition, the microbiota were strongly connected with intestinal SCFAs, lipase activity, and tight junctions, as shown by the Mantel test and Pearson's correlation. Taken together, according to Z-score, the ranking of advantageous functions among these protein diets was C. autoethanogenum diet > C. vulgaris diet > whole fishmeal diet > cottonseed protein concentrate > T. molitor diet. This study provides comprehensive data illustrating a mixed blessing effect of novel protein diets on the gut health of juvenile largemouth bass under an alternate feeding strategy.

Metal-driven bacterial community variation in urban and suburban park soils of Shanghai, China

Urban greenspaces, including parks, provide essential ecosystem services, and in which soil bacteria play vital roles in nutrient cycling, carbon sequestration, pollutant degradation, and promotion of the mental and physical well-being of residents. However, how did the bacterial distribution respond to the varying environmental variables along with urbanization in park soils remain unclear. In this study, by using Illumina Miseq sequencing combined with geochemistry analysis, the bacterial community structure and their response to soil variables were investigated in 30 parks from urban and suburban areas in Shanghai, China. The results showed that the soil organic matter (SOM), total nitrogen (TN), phosphorous (TP), chromium (Cr), copper (Cu), zinc (Zn), bioavailable potassium (AK), sulfur (AS), copper (ACu) and zinc (AZn) were significantly higher in urban park soils than suburban park soils. In contrast, the soil pH, EC, and bioavailable magnesium (AMg) in suburban park soils were significantly higher than those in urban park soils. Bacterial Shannon diversity was higher in suburban park soils than that of urban parks. Bacterial community structure between urban and suburban park soils showed a significant difference. Chloroflexi KD4-96, Chthonomonadetes, and Bacteroidia were significantly higher in suburban park soils, while Bacilli, Chloroflexi JG30-KF-CM66, and Clostridia were significantly enriched in urban park soils. The results of the Mantel test revealed that various metal concentrations, including Cd, AZn, Zn, ACu, Cu, Cr and AMg, had a significant impact on the bacterial communities in urban park soils, while Cd and K were determined to be the most influential factors shaping the bacterial communities in suburban park soils. The results of this study will help to further understand how the bacterial community responds to environmental variables in the city ecosystem.

Astragalus-cultivated soil was a suitable bed soil for nurturing Angelica sinensis seedlings from the rhizosphere microbiome perspective

Angelica sinensis (Oliv.) Diels is an important Chinese medicinal plant. A. sinensis seedlings are grown on an undisturbed alpine meadow soil to ensure the high-quality seedlings, but these soils are disappearing year after year. Thus, selecting a suitable bed soil for A. sinensis seedlings could ensure their long-term sustainability. Using HiSeq sequencing of 16S and 18S marker genes, we investigated the rhizosphere bacterial and fungal microbiotas of the seedlings grown in wheat, astragalus, potato, and angelica-cultivated soils at a geo-authentic habitat. Co-occurrence network analysis, canonical correspondence analysis, Mantel test, and Envfit test were used to examine the relationship between the microbiotas and the surrounding factors. Astragalus-cultivated soils exhibited the following properties: the highest plant weight, the highest neighborhood connectivity in the bacterial network, the highest ratio of positive/negative relationship in both bacterial and fungal networks, the highest relative abundance of the arbuscular mycorrhizal fungi and the ectomycorrhizal fungi, the lowest relative abundance of Rhizoctonia solani, the suitable soil pH, and the close relationship between the rhizosphere microbiotas and the ecological factors. Moreover, each growth stage has its own major drivers in all crop-cultivated soils. Climate temperature and soil pH at 56 days after planting, precipitation at 98 days, and plant weight as well as microbial biomass C and N at 129 days were the major drivers of the bacterial and fungal microbiotas. Overall, the astragalus-cultivated soil was a suitable bed soil for nurturing A. sinensis seedlings to replace the undisturbed alpine meadow soils.