Microbial diversity in cold seep sediments from the northern South China Sea

South China Sea （SCS） is the largest Western Pacific marginal sea. However, microbial studies have never been performed in the cold seep sediments in the SCS. In 2004, ＂SONNE＂ 177 cruise found two cold seep areas with different water depth in the northern SCS. Haiyang 4 area, where the water depth is around 3000 m, has already been confirmed for active seeping on the seafloor, such as microbial mats, authigenic carbonate crusts and bivalves. We investigated microbial abundance and diver- sity in a 5.55-m sediment core collected from this cold seep area. An integrated approach was employed including geochemistry and 16S rRNA gene phylogenetic analyses. Here, we show that microbial abun- dance and diversity along with geochemistry profiles of the sediment core revealed a coupled reaction between sulphate reduction and methane oxidation. Acridine orange direct count results showed that microbial abundance ranges from 105 to 106 cells/g sediment （wet weight）. The depth-related variation of the abundance showed the same trend as the methane concentration profile. Phylogenetic analysis indicated the presence of sulphate-reducing bacteria and anaerobic methane-oxidizing archaea. The diver- sity was much higher at the surface, but decreased sharply with depth in response to changes in the geochemical conditions of the sediments, such as methane, sulphate concentration and total organic carbon. Marine Benthic Group B, Chloroflexi and JS1 were predominant phylotypes of the archaeal and bacterial libraries, respectively.

Diversity of microbial plankton across the Three Gorges Dam of the Yangtze River,China

The Three Gorges Dam （TGD） of the Yangtze River, China, is one of the largest irrigation and hydroelectric engineering projects in the world. The effects of huge man-made projects like TGD on fauna and macrophyte are obvious, mainly through changes of water dynamics and flow pattern; however, it is less clear how microorganisms respond to such changes. This research was aimed to examine differences in microbial diversity at different seasons and locations （in front of and behind the TGD）. In addition, differences between particle-attached and free-living communities were also examined. The community structures of total and potentially active microorganisms in the water columns behind and in front of the TGD were analyzed with the DNA- and RNA-based 16S rRNA gene phylogenetic approaches over three different seasons. Clone libraries of 16S rRNA genes were prepared after ampli- fication from extracted DNA and, for some samples, after preparing cDNA from extracted rRNA. Differ- ences were observed between sites at different seasons and between free-living and particle-attached communities. Both bacterial and archaeal communities were more diverse in summer than in winter, due to higher nutrient levels and warmer temperature in summer than in winter. Particle-attached micro- organisms were more diverse than free-living communities, possibly because of higher nutrient levels and heterogeneous geochemical micro-environments in particles. Spatial variations in bacterial community structure were observed, i.e., the water reservoir behind the TGD （upstream） hosted more diverse bacte- rial populations than in front of the dam （downstream）, because of diverse sources of sediments and waters from upstream to the reservoir. These results have important implications for our understanding of responses of microbial communities to environmental changes in river ecosystems affected by dam construction.

Microbial diversity in two cold springs on the Qinghai-Tibetan Plateau

The microbial diversity in Wuli Area, Qinghai-Tibetan Plateau was investigated using 16S rRNA gene phylogenetic analyses. A total of 117 bacterial and 66 archaeal 16S rRNA gene clones were obtained from the Wuli cold springs, The bacterial clones could be classified into Proteobacteria, Acid- obacteria, Deinococci, Sphingobacteria, Flavobacteria, Nitrospirae, Actinobacteria, Gemmatimona- detes, and unclassified-bacteria; and the archaeal clones could be classified into Crenarchaeota and Thaumarchaeota. Among the major groups, Proteobacteria and Crenarchaeota were dominant in the bacterial and archaeal 16S rRNA gene clone libraries, respectively. The clone sequences obtained in Wuli cold springs were closely related to those from cold habitats, such as snow/ice/soils on high mountains or at high latitude. Especially, the microbial community composition of Wuli Area was more similar to that in Tibetan glaciers than cold environments of other locations. The data presented in this study have impli- cations for a better understanding of microbial diversity in cold springs on the Qinghai-Tibetan Plateau.

Distinguishing ectomycorrhizal and saprophytic fungi using carbon and nitrogen isotopic compositions

Ectomycorrhizal fungi, a group of widespread symbiotic fungi with plant, obtain carbon source from trees and improve plant mineral nutrient uptake with their widespread hyphal network. Ectomycorrhizal fungi can be used as inoculants to improve the survival rates of plantation. Saprophytic fungi use the nutrition from the debris of plant or animals, and it is difficult to distinguish the saprophytic and ectomycorrhizal fungi by morphological and anatomic methods. In this research, the differences of stable carbon and nitrogen isotopic compositions of these fungi were analyzed. The results showed that the abundances of 13C of were higher than those of ectomycorrhizal fungi and the abundances of 15N of saprophytic fungi were lower than those of ectomycorrhizal fungi. Such differences of stable carbon and nitrogen isotopic compositions between ectomycorrhizal fungi and saprophytic fungi can be ascribed to their different nutrition sources and ecological functions. These results collectively indicate that stable carbon and nitrogen isotopic compositions are an effective proxy for distinguishing between ectomycorrhizal and saprophytic fungi.

Microbial diversity in the hydrate-containing and-free surface sediments in the Shenhu area, South China Sea

Microbial diversity in the hydrate-containing （sites SH3B and SH7B） and -free （sites SHIB, SH5B, SH5C） sediments collected from the Shenhu area of the South China Sea （SCS） was investigated using 16S rRNA gene phylogenetic analysis. The phylogenetic results indicate difference in microbial communities be- tween hydrate-containing and -free sediments. At the gas hydrate-containing sites, bacterial communities were dominated by Deltaproteobacteria （30.5%）, and archaeal communities were dominated by Miscellaneous Crenarchaeotic Group （33.8%）; In contrast, Planctomycetes was the major group （43.9%） in bacterial communities, while Marine Benthic Group-D （MBG-D） （32.4%） took up the largest proportion in the archaeal communities. Moreover, the microbial communities have characteristics different from those in other hydrate-related sediments around the world, indicating that the presence of hydrates can affect the microbial distribution. In addition, the microbial community composition in the studied sediments has its own uniqueness, which may result from co-effect of geochemical characteristics and presence/absence of hydrate.

Biogeochemistry and geomicrobiology in extreme environments:Preface

1. IntroductionGeomicrobiology as an interdisciplinary area has achieved great progress during the past two decades （Dong and Yu, 2007）. Geomicrobiology involves the study of microbes in a number of fundamental geological processes, both in the past and present （Gadd, 2010）. Biogeochemistry in extreme geological environments is one of the key topics under this theme. The extreme environments include alkaline, acidic,

Research Progress and Challenges on Persistent Organic Pollutants in Lakes

Lakes are the main reservoirs of persistent organic pollutants(POPs)from land,atmo sphere and rivers.POPs in lakes undergo complex exchange,transformation,and degradation between water-air-sediment-biota interfaces,which are constrained and regulated by various physical,chemical and biological factors.POPs can affect ecological conditions,chemical properties of water and sedi ments,and biodiversity of the lake system.Therefore,it is important to study the sources,migration,transformation,environmental behavior and ecological impacts of POPs in lake ecosystems.This re view summarizes research progress on detection technologies,diversity and origins,historical records,migration and transformation,distribution patterns,degradation and toxic effects of POPs in lakes.Fi nally,future directions related to POPs in lakes were summarized.

贵州兴义喀斯特洞穴可培养放线菌多样性及抗菌活性初筛

【目的】进一步了解兴义喀斯特洞穴可培养放线菌资源及产活性代谢产物的能力。【方法】选取多种分离培养基,利用稀释直接涂布平板法对贵州黔西南兴义市多个喀斯特洞穴的土壤和岩石进行可培养放线菌资源分离;利用三种发酵培养基对相关放线菌进行生物产物初筛。【结果】根据16S rRNA基因序列的比对分析,将分离得到的251株放线菌分别归类到44个属,其中链霉菌属(Streptomyces)占分离菌株的比例为24.30%,小单孢菌属(Micromonospora)占比11.95%,红球菌属(Rhodococcus)占比9.16%,微杆菌属(Microbacterium)占比7.17%,诺卡氏菌属(Nocardia)占比6.37%,该五类放线菌为该地区可培养放线菌的优势菌群。对70株细菌进行活性次级代谢产物筛选,其中35株放线菌对指示菌具有抑制活性,且主要类群为链霉菌属和小单孢菌属。【结论】贵州兴义喀斯特洞穴中存在丰富多样的放线菌类群,且蕴藏大量具有产生活性次级代谢产物能力的菌株,为医药产业提供潜力菌株资源,极具进一步发掘和研究的价值。

Co-occurrence of nitrite-dependent anaerobic methane oxidizing and anaerobic ammonia oxidizing bacteria in two Qinghai-Tibetan saline lakes

Nitrite-dependent anaerobic methane-oxidiz- ing （n-damo） bacteria and anaerobic ammonia oxidizing （anammox） bacteria are two groups of microorganisms involved in global carbon and nitrogen cycling. In order to test whether the n-damo and anammox bacteria co-occur in natural saline environments, the DNA and cDNA samples obtained from the surficial sediments of two saline lakes （with salinity of 32 and 84 g/L, respectively） on the Tibetan Plateau were PCR-amplified with the use of anammox- and n-damo-specific primer sets, followed by clone library construction and phylogenetic analysis. DNA and cDNA- based clones affiliated with n-damo and anammox bacteria were successfully retrieved from the two samples, indicating that these two groups of bacteria can co-occur in natural saline environments with salinity as high as 84g/L. Our finding has great implications for our understanding of the global carbon and nitrogen cycle in nature.

A comprehensive census of lake microbial diversity on a global scale

Despite recent interest in microbial diversity and community structure of lakes across various spatial scales, a global biogeographic distribution pattern and its controlling factors have not been fully disclosed. Here, we compiled and analyzed 88,334,735 environmental 16S rRNA sequences from 431 lakes across a wide range of geographical distance and environmental conditions(in particular, salinity, 0–373.3 gL^–1). Our results showed that lake sediments inhabit significantly(ANOVA: P<0.001) more diverse microbial communities than lake waters. Non-metric dimensional scaling(NMDS) ordinations indicated that microbial community compositions differed distinctly among sample types(freshwater vs. saline, water vs. sediment) and geographic locations. Mantel and partial Mantel tests showed that microbial community composition in lake water was significantly(P=0.001) correlated with geographic distance, salinity, and pH. Statistical analyses based on neutral community and null models indicated that stochastic processes may play predominant roles in shaping the microbial biogeographic distribution patterns in the studied global lake waters. The dispersal-related stochasticity(e.g., homogenizing dispersal) exhibited a stronger influence on the distribution of microbial community in freshwater lakes than in saline lakes. Overall, this work expands our understanding of the impact of geographic distance, environmental conditions, and stochastic processes on microbial distribution in global lakes.

Microbial diversity accumulates in a downstream direction in the Three Gorges Reservoir

Organic and inorganic materials migrate downstream and have important roles in regulating environmental health in the river networks.However,it remains unclear whether and how a mixture of materials(i.e.,microbial species)from various upstream habitats contribute to microbial community coalescence upstream of a dam.Here we track the spatial variation in microbial abundance and diversity in the Three Gorges Reservoir based on quantitative PCR and 16 S rRNA gene high-throughput sequencing data.We further quantitatively assess the relative contributions of microbial species from mainstem,its tributaries,and the surrounding riverbank soils to the area immediately upstream of the Three Gorges Dam(TGD).We found an increase of microbial diversity and the convergent microbial distribution pattern in areas immediately upstream of TGD,suggesting this area become a new confluence for microbial diversity immigrating from upstream.Indeed,the number of shared species increased from upstream to TGD but unique species decreased,indicating immigration of various sources of microbial species overwhelms local environmental conditions in structuring microbial community close to TGD.By quantifying the sources of microbial species close to TGD,we found little contribution from soils as compared to tributaries,especially for sites closer to TGD,suggesting tributary microbes have greater influence on microbial diversity and environmental health in the Three Gorges Reservoir.Collectively,our results suggest that tracking microbial geographic origin and evaluating accumulating effects of microbial diversity shed light on the ecological processes in microbial communities and provide information for regulating aquatic ecological health.

Seasonal Interaction of River Water-Groundwater-Salt Lake Brine and Its Influence on Water-Salt Balance in the Nalenggele River Catchment in Qaidam Basin,NW China

Identifying interactions among river water,groundwater and salt lake brine is important for sustainable exploitation of brine mineral resources.In this study,we investigated the water exchange rate in dry and wet seasons,and assessed the influence of seasonal water exchange on brine concentration and crystallization process in the Nalenggele(NLGL)catchment of Qaidam Basin,China.The results show that the surface water infiltration and groundwater recharge rates in the wet season were 2.81×10^(-3)and 1.15×10^(-3)m^(3)/(s·m)in upstream,1.63×10^(-2)and 1.53×10^(-2)m^(3)/(s·m)in midstream,and 2.83×10^(-4)and 6.82×10^(-5)m^(3)/(s·m)in downstream,respectively;while their counterparts in the dry season were 9.81×10^(-4)and 5.05×10^(-4)m^(3)/(s·m)in upstream,and 8.34×10^(-3)and 7.78×10^(-3)m^(3)/(s·m)in midstream,respectively.The water exchange strongly influenced brine concentration and crystallinzation process,with brine chemistry belonging to 3K_(2)SO_(4)·Na_(2)SO_(4) and KCl types in wet and dry seasons,respectively.The strong water exchange in wet season destroyed the water-salt balance,while the low water exchange rate in dry season facilitated preparation of KCl products.

Source Analysis of Lithium Deposit in Dong-Xi-Taijinaier Salt Lake of Qaidam Basin,Qinghai-Tibet Plateau

The Dong-Xi-Taijinaier Salt Lake(DXTSL) of Qaidam Basin is known as one of rich lithium reserves in China.However,the source of lithium deposits in this region remains unclear.The hydrochemistry and lithium isotopes(δ7Li) of water and solid samples along the Nalenggele River catchment were studied in combination with rock leaching experiments.The results showed the hot springs in the upstream contained high content of lithium and ratio of Li × 1 000/total dissolved solids(1.5–3.5),but the lower δ7Li values(4.33‰–11.59‰),meaning that it is one important lithium sources.The leaching experiments by the rich-lithium volcanic rocks(average content of 474.7 mg/kg) showed that under temperature of 20–80 ℃ and long time duration(24–96 h),the concentration of lithium released by leaching of the sampled volcanic rocks increased from 0.58 to 1.49 mg/L,with the leaching rate decreasing from 0.024 to 0.015 mg/(L·h) and the corresponding lithium release rate increasing from 29% to 74%.Calculation based on water-salt balance showed that the total amount of lithium contribution from hydrothermal fluids and volcanic rock weathering is about 4.99 and 0.29 Mt since 13.1 ka,respectively.Therefore,hot springs and leaching of volcanic rocks are main contributors to lithium deposit in DXTSL.

Abundance and diversity of candidate division JSl- and Chloroflexi-related bacteria in cold seep sediments of the northern South China Sea

Candidate division JS 1-and Chloroflexi-related bacteria are ubiquitous in various deep marine sediments worldwide, yet almost nothing is known about their abundance and diversity in cold seep sediments. Here, we investigated the abundance and diversity of JS1- and Chloroflexi-related bacteria in a cold seep marine sediment core collected from the northern South China Sea （SCS） with the employment of quantitative polymerase chain reaction （qPCR） and 16S rRNA gene phylogenetic analyses. The qPCR results showed that 16S rRNA gene copies per gram of sediments for the total bacteria and JS 1- and Chloroflexi-related bacteria were at magnitudes of 108 and 106, respectively. The relative abundance of JS 1- and Chloroflexi-related 16S rRNA genes to that of total bacteria was 0.07%-8.78% throughout the core. Phyloge- netic analyses showed that the JS-1 related clone sequences were dominant throughout the core. Our study provided insights into abundance and diversity of JS 1- and Chloroflexi-related bacteria in the northern SCS cold seep sediments.

Distinct Assembly Mechanisms for Prokaryotic and Microeukaryotic Communities in the Water of Qinghai Lake

Assembly processes of prokaryotic and microeukaryotic community is an important issue in microbial ecology.However,unclear remains about the relative contribution of deterministic and stochastic processes to the shaping of prokaryotic and microeukaryotic communities in saline lake water.Here,we systematically investigated the assembly processes governing the prokaryotic and microeukaryotic communities in Qinghai Lake with the use of Illumina sequencing and a null model.The results showed that both deterministic and stochastic processes play vital roles in shaping the assemblies of prokaryotic and microeukaryotic communities,in which stochastic processes appeared to dominate(> 70%).Prokaryotic communities were mainly governed by non-dominant processes(60.4%),followed by homogeneous selection(15.8%),variable selection(13.6%) and dispersal limitation(10.2%),whereas microeukaryotes were strongly driven by non-dominant processes(68.9%),followed by variable selection(23.6%) and homogenizing dispersal(6.3%).In terms of variable selection,nutrients(e.g.,ammonium,dissolved inorganic carbon,dissolved organic carbon and total nitrogen) were the major factors influencing prokaryotic and microeukaryotic community structures.In summary,prokaryotes and microeukaryotes can be predominantly structured by different assembly mechanisms,in which stochasticity is stronger than deterministic processes.This finding helps to better comprehend the assembly of prokaryotic and eukaryotic communities in saline lakes.

Gut Microbiome Variation Along A Lifestyle Gradient Reveals Threats Faced by Asian Elephants

The gut microbiome is closely related to host nutrition and health.However,the relationships between gut microorganisms and host lifestyle are not well characterized.In the absence of confounding geographic variation,we defined clear patterns of variation in the gut microbiomes of Asian elephants(AEs)in the Wild Elephant Valley,Xishuangbanna,China,along a lifestyle gradient(completely captive,semicaptive,semiwild,and completely wild).A phylogenetic analysis using the 16S rRNA gene sequences highlighted that the microbial diversity decreased as the degree of captivity increased.Furthermore,the results showed that the bacterial taxon WCHB1-41_c was substantially affected by lifestyle variations.qRT-PCR analysis revealed a paucity of genes related to butyrate production in the gut microbiome of AEs with a completely wild lifestyle,which may be due to the increased unfavorable environmental factors.Overall,these results demonstrate the distinct gut microbiome characteristics among AEs with a gradient of lifestyles and provide a basis for designing strategies to improve the well-being or conservation of this important animal species.

Biological and Pollution Aerosols on Snow and Ice--Interplay between the Atmosphere and the Cryosphere

1 BACKGROUND The cryosphere covers a relevant portion of the Earth’s surface,playing a major role for terrestrial and marine biomes(Bosson et al.,2023;Sands et al.,2023;Anesio et al.,2017).Glacierets,glaciers and ice sheets represent together 10%of the global land surface,while the annual average maximum of snow cover during the winter accounts for up to 49%of the Northern Hemisphere’s surface (Qin,2017).Aerosols are another major component of the Earth system,playing pivotal roles in the biogeochemical cycles and in the Earth radiative mass balance (Bellouin et al.,2020;Carslaw et al.,2010).A complex network of interactions links aerosols and glaciers.