Linking soil organic carbon mineralization to soil physicochemical properties and bacterial alpha diversity at different depths following land use changes

Background Anthropogenic land use changes(LUCs)impart intensifying impacts on soil organic carbon(SOC)turnover,leading to uncertainty concerning SOC mineralization patterns and determining whether soils act as“source”or“sink”in the global carbon budget.Therefore,understanding the SOC mineralization characteristics of different LUC patterns and their potential influencing factors is crucial.An indoor incubation experiment was conducted to study the SOC mineralization patterns and their relevance to soil physicochemical properties,soil enzyme activity,SOC fractions,and bacterial alpha diversity.The soils were collected from two layers of five typical LUC patterns in Yellow Sea Forest Park,including four that were converted from wheat-corn rotation systems[a gingko plantation(G),a metasequoia plantation(M),a gingko-wheat-corn agroforestry system(GW),and a gingko-metasequoia system(GM)]and a traditional wheat-corn system(W).Results LUCs had significant and diverse impacts on the SOC content and SOC fraction contents and on soil enzyme activity.The cumulative SOC mineralization was significantly higher in the M systen than in the W and GW systems at 0-20 cm depth and higher in the G system than in the GW system at 20-40 cm depth after 60-day incubation.The mineralization ratio was highest in the W system and lowest in the GW system.The soil pH and bulk density had a significant negative correlation with the cumulative SOC mineralization,while the soil bacterial Shannon index had a significant positive correlation with cumulative SOC mineralization.Multiple stepwise linear regression analysis showed that the SOC mineralization potential was dominantly explained by the bacterial Shannon index and operational taxonomic units(OTUs).The GW system had lower potentially mineralizable SOC and higher SOC stability.Additionally,the incubation time and cumulative SOC mineralization were well fitted by the first-order kinetic equation.Conclusions LUCs significantly changed SOC mineralization characteristics and the results highlighted the important roles of the bacterial community in soil carbon cycling,which contributes to the fundamental understanding of SOC turnover regulation.

How many species of Apodemus and Rattus occur in China？ A survey based on mitochondrial cyt b and morphological analyses

Apodemus （mice） and Rattus （rats） are the top rodent reservoirs for zoonoses in China,yet little is known about their diversity.We reexamined the alpha diversity of these two genera based on a new collection of specimens from China and their cyt b sequences in GenBank.We also tested whether species could be identified using external and craniodental measurements exclusively.Measurements from 147 specimens of Apodemus and 233 specimens of Rattus were used for morphological comparisons.We analysed 74 cyt b sequences of Apodemus and 100 cyt b sequences of Rattus to facilitate phylogenetic estimations.Results demonstrated that nine species of Apodemus and seven species of Rattus,plus a new subspecies of Rattus nitidus,are distributed in China.Principal component analysis using external and craniodental measurements revealed that measurements alone could not separate the recognized species.The occurrence of Rattus pyctoris in China remains uncertain.

Performance comparison of different microbial DNA extraction methods on bird feces

Background:As an important player during food digestion,gut microbiota has attracted much attention in diet adaptation studies in birds.Microbiota extracted from feces has been widely used as a proxy for gut microbiota.Although several methods have been developed for microbial DNA extraction,their performances in the bird feces have not been systematacially evaluated yet.Methods:In this study,we applied three DNA extraction methods(Qiagen,MoBio and Bead)to extract DNA from feces of three avian dietary guilds(granivore,omnivore and carnivore),sequenced V4 region of 16S rRNA gene for each extract and evaluated the performances of DNA yield,DNA integrity,microbial composition,cell lysis capacity and alpha diversity for the three methods on each dietary guild.Results:Bead method was the best on the performance of both DNA yield and DNA integrity regardless of dietary guild.In granivore,microbial relative abundance at both species and phylum levels,alpha diversity and cell lysis capacity were comparable among all methods.In omnivore,Qiagen had the best performance on alpha diversity,fol-lowed by Bead and MoBio.There were small variations on microbial relative abundance at both species and phylum levels among different extraction methods.MoBio exhibited the best performance on cell lysis capacity.In carnivore,considerable variations were found on microbial relative abundance at both species and phylum levels.Qiagen had the best performance on alpha diversity,followed by MoBio and Bead.MoBio had the highest cell lysis capacity.Conclusions:DNA yield and integrity have no obvious impact on microbial composition,alpha diversity or cell lysis capacity.The microbiota results(e.g.,microbial composition,cell lysis capacity,alpha diversity)obtained from differ-ent methods are comparable in granivorous avian species but not in omnivorous or carnivorous birds.Either method could be used in granivore microbiota studies.For omnivores and carnivores,we recommend Qiagen method when the research purpose is microbial diversity and MoBio when gram-positive bacteria is the research target.

Local and regional richness and rarity of leaf-litter ants:An overview from spacial scale in neotropical region

An unusual approach about richness and rarity of leaf-litter ant species is presented here from a dry forest reminiscent in Pantanal province (Chacoan subregion) suggesting the boundaries that defining local and regional scales for this particular ant community. We analysed the frequency of distribution of 170 ant species collected on 262 Winkler’s samples along Serra da Bodoquena National Park, Mato Grosso do Sul state, Brazil and described some ecological mechanisms that made the species richness estimates be highly influenced by species with low frequencies of records in an extent regional of a pristine dry forest. Bayesian inference was conducted to provide if the probability of latitudinal gradient was correlated with the species richness to define alpha diversity.

Taxonomic, functional, and phylogenetic diversity patterns reveal different processes shaping river fish assemblages in the Eastern Huai River Basin, China

Understanding contributions of different environmental drivers to the structure and function of river biota is critical for biodiversity and environmental conservation.Yet,there is no consensus on which drivers have the greatest impact on fish diversity,especially in watersheds disturbed by multiple human activities.Fish taxonomic,phylogenetic,and functional diversity at both alpha and beta dimensions and their environmental drivers were studied in a total of 84 river sites from three watersheds,Huai River watershed(HRW),Sui River watershed(SRW),and Yishusi River watershed(YRW)in the Eastern Huai River Basin of China.Results showed that rivers in the three watersheds had no significant difference in both taxonomic and functional alpha diversity.Rivers in the HRW had significantly higher phylogenetic alpha diversity.For taxonomic and phylogenetic beta diversity,the overall beta diversity and turnover component were significant higher in the HRW.For functional beta diversity,the overall beta diversity was significantly lower in the HRW.Multiple linear regression(MLR)and redundancy analysis(RDA)showed that local(e.g.,nutrients,dissolved oxygen,river width,transparency),regional(e.g.,wetland),climate(e.g.,temperature),and spatial variables structured alpha and beta fish diversity.Variation partitioning analysis indicated that the pure contributions of local and spatial variables were more important than that of climate and regional variables,which suggested that spatial effects and local environmental filtering were the main factors driving the beta diversity of fish assemblages in these rivers.The current study highlights the importance of considering multidimensional diversity and multiple environmental factors for conserving river fishes.

Effects of microplastic polystyrene,simulated acid rain and arbuscular mycorrhizal fungi on Trifolium repens growth and soil microbial community composition

Microplastic pollution is a global and ubiquitous environmental problem in the oceans as well as in the terrestrial environment.We examined the fate of microplastic polystyrene(MPS)beads in experimental soil in the presence and absence of symbiotic arbuscular mycorrhizal fungi(AMF)and simulated acid rain(SAR)to determine whether the combinations of these three factors altered the growth of white clover Trifolium repens.We found that MPS,SAR,or AMF added singly to soil did not alter T.repens growth or yields.In contrast,MPS and AMF together significantly reduced shoot biomass,while SAR and MPS together significantly reduced soil available phosphorus independent of AMF presence.Microplastic polystyrene,AMF,and SAR together significantly reduced soil NO_(3)^(-)-N.Arbuscular mycorrhizal fungi added singly also enriched the beneficial soil bacteria(genus Solirubrobacter),while MPS combined with AMF significantly enriched the potential plant pathogenic fungus Spiromastix.Arbuscular mycorrhizal fungi inoculation with MPS increased the abundance of soil hydrocarbon degraders independent of the presence of SAR.In addition,the abundance of soil nitrate reducers was increased by MPS,especially in the presence of AMF and SAR.Moreover,SAR alone increased the abundance of soil pathogens within the fungal community including antibiotic producers.These findings indicate that the coexistence of MPS,SAR,and AMF may exacerbate the adverse effects of MPS on soil and plant health.

Phylogenetic structure and phylogenetic diversity of angiosperm assemblages in forests along an elevational gradient in Changbaishan,

Aims Understanding what drives the variation in species composition and diversity among local communities can provide insights into the mechanisms of community assembly.Because ecological traits are often thought to be phylogenetically conserved,there should be patterns in phylogenetic structure and phylogenetic diversity in local communities along ecological gradients.We investigate potential patterns in angiosperm assemblages along an elevational gradient with a steep ecological gradient in Changbaishan,China.Methods We used 13 angiosperm assemblages in forest plots(32×32 m)distributed along an elevational gradient from 720 to 1900 m above sea level.We used Faith’s phylogenetic diversity metric to quantify the phylogenetic alpha diversity of each forest plot,used the net relatedness index to quantify the degree of phylogenetic relatedness among angiosperm species within each forest plot and used a phylogenetic dissimilarity index to quantify phylogenetic beta diversity among forest plots.We related the measures of phylogenetic structure and phylogenetic diversity to environmental(climatic and edaphic)factors.Important Findings Our study showed that angiosperm assemblages tended to be more phylogenetically clustered at higher elevations in Changbaishan.This finding is consistent with the prediction of the phylogenetic niche conservatism hypothesis,which highlights the role of niche constraints in governing the phylogenetic structure of assemblages.Our study also showed that woody assemblages differ from herbaceous assemblages in several major aspects.First,phylogenetic clustering dominated in woody assemblages,whereas phylogenetic overdispersion dominated in herbaceous assemblages;second,patterns in phylogenetic relatedness along the elevational and temperature gradients of Changbaishan were stronger for woody assemblages than for herbaceous assemblages;third,environmental variables explained much more variations in phylogenetic relatedness,phylogenetic alpha diversity and phylogenetic beta diversity for woody assemblages than for herbaceous assemblages.

High‑throughput sequencing view on the magnitude of global fungal diversity

High-throughput DNA sequencing has dramatically transformed several areas of biodiversity research including mycol-ogy.Despite limitations,high-throughput sequencing is nowadays a predominant method to characterize the alpha and beta diversity of fungal communities.Across the papers utilizing high-throughput sequencing approaches to study natural habitats in terrestrial ecosystems worldwide,>200 studies published until 2019 have generated over 250 million sequences of the primary mycological metabarcoding marker,the nuclear ribosomal internal transcribed spacer 2(ITS2).Here we show that at a 97%sequence similarity threshold,the total richness of non-singleton fungal taxa across the studies published so far is 1.08 million,mostly Ascomycota(56.8%of the taxa)and Basidiomycota(36.7%of the taxa).The Chao-1 estimate of the total extant fungal diversity based on this dataset is 6.28 million taxa,representing a conservative estimate of global fungal species richness.Soil and litter represent the habitats with the highest alpha diversity of fungi followed by air,plant shoots,plant roots and deadwood with Chao-1 predictions,for samples containing 5000 sequences,of 1219,569,392,228,215 and 140 molecular species,respectively.Based on the high-throughput sequencing data,the highest proportion of unknown fungal species is associated with samples of lichen and plant tissues.When considering the use of high-throughput sequenc-ing for the estimation of global fungal diversity,the limitations of the method have to be taken into account,some of which are sequencing platform-specific while others are inherent to the metabarcoding approaches of species representation.In this respect,high-throughput sequencing data can complement fungal diversity predictions based on methods of traditional mycology and increase our understanding of fungal biodiversity.

Bacterial communities in paddy soils changed by milk vetch as green manure: A study conducted across six provinces in South China

The use of green manures contributes to sustainable soil and nutrient management in agriculture;however, the responses of soil microbial communities to different fertilization regimes at the regional scale are uncertain. A study was undertaken across multiple sites and years in Hunan, Jiangxi, Anhui, Henan,Hubei, and Fujian provinces of South China to investigate the effects of green manuring on the structure and function of soil bacterial communities in rice-green manure cropping systems. The study included four treatments: winter fallow with no chemical fertilizer as a control(NF), milk vetch as green manure without chemical fertilizer(GM), winter fallow and chemical fertilizer(CF), and a combination of chemical fertilizer and milk vetch(GMCF).Significant differences were found in the responses of soil microbial communities at different sites, with sampling sites explaining 72.33%(F = 36.59,P = 0.001) of the community composition variation. The bacterial communities in the soils from Anhui, Henan, and Hubei were broadly similar, while those from Hunan were distinctly different from other locations. The analysis of Weighted UniFrac distances showed that milk vetch changed soil microbial communities compared with winter fallow. Proteobacteria and Chloroflexi predominated in these paddy soils;however, the application of green manures increased the relative abundance of Actinobacteria. There was evidence showing that the functional microbes which play important roles in the cycling of soil carbon, nitrogen(N), and sulfur(S) changed after several years of milk vetch utilization(linear discriminant analysis score > 2). The abundance of methane-oxidizing bacteria and S-reducing bacteria increased, and microbes involved in N fixation, nitrification, and denitrification also increased in some provinces. We concluded that the application of milk vetch changed the bacterial community structure and affected the functional groups related to nutrient transformation in soils at a regional scale.

Microbiome data analysis with applications to pre-clinical studies using QIIME2: Statistical considerations

Diversity analysis and taxonomic profiles can be generated from marker-gene sequence data with the help of many available computational tools.The Quantitative Insights into Microbial Ecology Version 2(QIIME2)has been widely used for 16S rRNA data analysis.While many articles have demonstrated the use of QIIME2 with suitable datasets,the application to preclinical data has rarely been talked about.The issues involved in the pre-clinical data include the low-quality score and small sample size that should be addressed properly during analysis.In addition,there are few articles that discuss the detailed statistical methods behind those alpha and beta diversity significance tests that researchers are eager to find.Running the program without knowing the logic behind it is extremely risky.In this article,we first provide a guideline for analyzing 16S rRNA data using QIIME2.Then we will talk about issues in pre-clinical data,and how they could impact the outcome.Finally,we provide brief explanations of statistical methods such as group significance tests and sample size calculation.