Urbanization strengthens the edge effects on species diversity and composition of woody plants in remnant forests

Background:Urban remnant forests are embedded in urban areas and are threatened directly and indirectly by urbanization.The direct effects(e.g.,loss of area)have been well studied.However,knowledge about the indirect influence of urbanization through edge effects on the biodiversity in remnant forests is limited.Methods:In this study,we surveyed woody plant species in 72 plots in nine remnant forest patches in Guiyang,China.We examined the influences of urbanization and edge effects on the species diversity and composition of woody plants in remnant forests.We compared alpha diversities and quantified compositional dissimilarities in interior and edge sites at different levels of urbanization.We also measured the niche width of the recorded plant species and assessed whether high levels of urbanization and edge effects increased the number of generalist species.Results and conclusions:The Shannon index,the Simpson index and the Pielou index of adult trees were lowest in the edge habitat under high levels of urbanization.Significant differences in the Shannon index and the Simpson index of sapling/seedling were detected between interior and edge sites under low urbanization.The edge effects on the species composition of adult trees were intensified by high levels of urbanization.Woody plant species with wide niche widths were more abundant at edge sites under high levels of urbanization.Therefore,we recommend that urban expansion surrounding remnant patches should be strictly controlled to alleviate edge effects on biodiversity.

Environmental drivers of soil microbial activity and diversity along an elevational gradient

Microbial functional and structural patterns and drivers along elevational gradients have recently received increasing attention.In this study,we examined soil bacterial and fungal community diversity,compositions,and microbial activities(i.e.,soil basal respiration and extracellular enzyme activities)across an elevational gradient from 1148 m to 2080 m(consists of six elevations)in the Yuanmou dry-hot valley located in Southwest China.Environmental factors,including soil temperature,moisture content,pH,soil organic carbon(SOC),total nitrogen(TN),the C/N ratio,total phosphorus(TP),and aboveground plant biomass were also determined.The results showed that soil bacterial alpha diversity(Shannon index)was unaffected by elevation,whereas fungal alpha diversity firstly increased significantly from 1148 m to 1539 m but did not increase further at higher elevations.Bacterial Shannon index was significantly correlated with SOC,whereas fungal Shannon index was remarkably associated with soil temperature.Microbial activity,beta diversities and community composition varied with elevation,but none of them showed a consistent trend.Monte Carlo test revealed that soil moisture followed by temperature,and pH,were the primary drivers of bacterial community composition.Soil fungal community composition significantly depended on soil moisture.Overall,our study suggested bacterial diversity and composition were determined by climatic(moisture and temperature)and edaphic properties(SOC and pH),while fungal diversity and composition were structured mainly by climatic factors.These findings may contribute to a better understanding of microbial responses along elevational gradients in this semi-arid region.

Forest succession trajectories after fi res in valleys and on slopes in the Greater Khingan Mountains,China

Accurate assessment of postfire vegetation recovery is important for forest management and the conservation of species diversity.Topography is an important factor aff ecting vegetation recovery but whether species composition varies with diff erent recovery stages and between valleys and slopes is unclear.Using fi eld data and a space-for-time substitution method,we quantifi ed species richness and diversity to obtain the successional trajectories of valleys and slopes.We surveyed the species of 10 burned areas from 1986 to 2010 in the Greater Khingan Mountains in northeastern China,and found that with increasing postfi re recovery time,species richness in both valleys and slopes gradually decreased.However,species richness in valleys was relatively higher.Shrubs recovered rapidly in the valleys,and species diversity maximized approximately 11 years after fi re.However,it maximized 17–18 years after fi re on the slopes.Numerous shade-tolerant species were present in the valleys 11 years after fi re but not until after 18 years on slopes.Larch appeared earlier than 11 years after fi re and its recovery was slow in the valleys but appeared quickly on slopes and established dominance early.Our study provides some new insights into vegetation succession after fi re at local scales.After fi re,the vegetation recovery processes diff er with topography and it aff ects the initial rate of recovery and species composition at diff erent successional stages.

Development and applications of functional gene microarrays in the analysis of the functional diversity,composition,and structure of microbial communities

Functional gene arrays(FGAs)are a special type of microarrays containing probes for key genes involved in microbial functional processes,such as biogeochemical cycling of carbon,nitrogen,sulfur,phosphorus,and metals,biodegradation of environmental contaminants,energy processing,and stress responses.GeoChips are considered as the most comprehensive FGAs.Experimentally established probe design criteria and a computational pipeline integrating sequence retrieval,probe design and verification,array construction,data analysis,and automatic update are used to develop the GeoChip technology.GeoChip has been systematically evaluated and demonstrated to be a powerful tool for rapid,specific,sensitive,and quantitative analysis of microbial communities in a high-throughput manner.Several generations of GeoChip have been developed and applied to investigate the functional diversity,composition,structure,function,and dynamics of a variety of microbial communities from different habitats,such as water,soil,marine,bioreactor,human microbiome,and extreme ecosystems.GeoChip is able to address fundamental questions related to global change,bioenergy,bioremediation,agricultural operation,land use,human health,environmental restoration,and ecological theories and to link the microbial community structure to environmental factors and ecosystem functioning.

Metagenomic Analysis of Mangshan Pit Viper (Protobothrops mangshanensis) Gut Microbiota Reveals Differences among Wild and Captive Individuals Linked to Hibernating Behaviors

Gut microbiota play important roles in the immunity,digestion,and energy meta bolism of their reptile hosts.Mangshan pit viper(Protobothrops mangshanensis)is a critically endangered snake species that is a Class I national protected species in China.Little is known regarding the relationship between P.mangshanensis and their gut microbial communities.In this study,the gut microbiota of wild P.mangshanensis individuals,artificially hiberna ting captive individuals,and non-hibernating captive individuals were compared across nine samples.Comparative shotgun metagenomic analysis was used to investigate the taxonomic composition,diversity,and function of P.mangshanensis gut microbial communities and assess whether their gut microbiomes were affected by their living environments and captivity conditions.The dominant phyla within P.mangshanensis gut microbial communities were Proteobacteria(65.55%),Bacteroidetes(15.97%),and Firmicutes(8.11%).Enriched functional pathways within the gut microbiota included meta bolism(54.9%),environmental information processing(9.67%),and genetic information processing(9.37%).Wild snake gut communities exhibited higher microbial diversity than the other two groups.The gut microbiomes of wild and hibernating captive snakes may be more reflective of healthy intestinal homeostasis than that in nonhibernating snakes.Specifically,non-hibernating snakes exhibited increased levelsof potentially pathogenic populations and functional specialization within gut microbial communities.Thus,different livingenvironments and captivitymethodsmay correspond to major shifts in microbiota composition,diversity,and function within P.mangshanensis.This study provides important insights to help guide the conservation of P.mangshanensis,while also carrying broad implications for our understanding of the effects of living environments and non-hibernating captivity conditions on the gut microbiota of snakes.