陕北地区苹果树根内细菌多样性分析

以延安市4个不同县区苹果树根为研究对象，分析苹果树根内生细菌的群落组成和多样性，揭示内生细菌的群落结构及多样性差异。采用高通量测序技术分析4个不同县区苹果树根内生细菌16S rRNA基因V3~V4 变异区序列，使用生物信息学方法分析其内生细菌的群落结构及多样性。结果表明，测序共获得994 571条有效序列，在97%一致性下共产生1 559个有效的操作分类单元(operational taxonomic uunits，OTUs)。在门水平上，4个样地苹果树根内生细菌群落组成中共有的优势类群分别为放线菌门(Actinobacteria)和变形菌门(Proteobacteria)，其相对丰富度分别为33.1%~60.7%和30.9%~61.6%；属水平上的优势菌属为假单胞菌属(Pseudomonas)、节杆菌属(Arthrobacter)、链霉菌属(Streptomyces)、诺卡氏菌属(Nocardioides)、叶杆菌属(Phyllobacterium)、黄杆菌属(Flavobacterium)、农杆菌属(Agrobacterium)和贪噬菌属(Variovorax)。Alpha多样性和Beta多样性分析表明，宜川县(YC)的Chao1指数(433.54)和Shannon指数(6.45)最大，基于韦恩图分析4个样地苹果树根内生细菌群落存在354个共有OTUs，延长县(YS)、宝塔区(BT)、宜川县(YC)、洛川县(LC)独有苹果树根内生细菌群落的OTUs分别为378、430、486和477。典范对应分析(Canonical Correlation Analysis, CCA)结果表明，土壤pH是影响4个样地苹果树根内生细菌的群落多样性变化的主要因素。4个样地苹果树根内生细菌种类丰富，但群落结构组成和丰富度的差异不明显，功能预测分析表明无论是Level 1还是Level 2，均未发现显著性差异的代谢通路，此结果表明苹果树根系招募了特异型有益的内生细菌菌群。本研究可为苹果树根内生细菌菌种资源的开发和应用提供参考。     

赤眼蜂与柞蚕卵共生细菌群落分析及功能预测

为了探明柞蚕（Antheraea pernyi）卵与赤眼蜂(Trichogramma)之间内共生菌的相互联系，通过16S rRNA高通量测序技术对赤眼蜂和柞蚕卵的内共生菌多样性及相对丰度进行了测定，并通过KEGG和COG分析了内共生菌生物群落代谢途径差异，预测了生物群落蛋白功能。结果表明，柞蚕卵内共生菌物种丰度在各级分类单元上均高于赤眼蜂，二者共有内共生菌为肠杆菌属（Enterobacter）、假单胞菌(Pseudomonas)、泛菌属(Pantoea)、埃希氏杆菌-志贺氏菌属（Escherichia-Shigella）、芽胞杆菌属（Bacillus）和鞘氨醇单胞菌属（Sphingomonas），除芽胞杆菌属隶属于厚壁菌门(Firmicute)外，其他均隶属于变形菌门γ-变形菌纲（γ-proteobacteria）。就相对丰度而言，赤眼蜂体内葡萄球菌属(Staphylococcus)分布量最高，而柞蚕卵内不动杆菌属(Acinetobacter)分布量最高。KEGG代谢途径差异分析表明，微生物群落功能主要为氨基酸和碳水化合物代谢，但不同代谢功能的强弱有差异。COG生物群落蛋白功能预测表明，赤眼蜂内共生菌群落蛋白质的氨基酸转运代谢功能显著强于柞蚕卵，但是柞蚕卵内共生菌群落蛋白的脂质转运代谢功能和信号传导功能显著强于赤眼蜂。尽管赤眼蜂和柞蚕卵内共生菌的丰度和多样性有差异，但二者存在多种共有共生菌，这些共有共生菌为次生共生菌，参与了赤眼蜂和柞蚕卵的氨基酸代谢功能、碳水化合物代谢功能以及胞膜转运功能等，因此可能在柞蚕卵和赤眼蜂之间进行平行传递。     

火棘不同组织内生细菌群落多样性

为了解火棘不同组织内生细菌群落多样性,该研究采用高通量测序技术对火棘内生细菌16S rRNA V5～V7可变区进行测序,分析火棘不同组织部位内生细菌群落多样性。结果表明:(1)从火棘根、茎、叶组织中共获得内生细菌OTU 1 818个,其中根部754个,茎部 308 个,叶部756个,三者共有 OTU 152 个。(2)物种分类显示,不同火棘组织内生细菌具有丰富的群落多样性,火棘根部内生细菌种类隶属于23门53纲137目216科373属557种,其中异样根瘤菌属(Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium)和链霉菌属(Streptomyces)为优势属,其相对丰度分别为 10.57%和 8.00%; 茎部内生细菌种类隶属于21门32纲76目126科204属270种,其中马赛菌属(Massilia)和未知分类的丛毛单胞菌科属(unclassified_f_Comamonadaceae)为优势属,其相对丰度分别为31.10%和12.82%; 叶部内生细菌种类隶属于21门52纲130目210科380属581种,其中土芽孢杆菌属(Geobacillus)和假单胞菌属(Pseudomonas)为优势属,其相对丰度分别为12.31%和9.84%。(3)PICRUSt功能预测表明,根部内生细菌物种最丰富,参与各种代谢调控的细菌丰度最高。该研究结果为进一步探讨植物内生细菌功能,挖掘新的有益微生物资源提供了参考。     

利用高通量测序技术对水稻秸秆中、低温降解菌系的比较分析

采用Illumina MiSeq高通量测序技术,对中、低温（中温25 ℃、低温10 ℃）富集驯化所得水稻秸秆降解菌系进行测序;采用生物信息学方法对中、低温秸秆降解菌系群落生物多样性进行分析。结果表明,测序质控后获得601 489条16S rDNA序列,平均长度273 bp,经Silval 132数据库比对,中温降解菌系包括18个门,172个属,302个OTU,其中优势菌属为弓形杆菌属（Arcobacter）、拟杆菌属（Bacteroides）、屠场杆菌属（Macellibacteroides）、假单胞菌属（Pseudomonas）和梭形杆菌属（Lysinibacillus）;低温降解菌系包括16个门,169个属,280个OTU,其中优势菌属为弓形杆菌属、屠场杆菌属、拟杆菌属、丛毛单胞属（Comamonas）和假单胞菌属。温度对降解菌系中优势菌门的相对丰度无显著影响,中、低温秸秆降解菌系主要菌属相对丰度差异显著。     

生物有机肥对菠萝心腐病及根际土壤细菌群落的影响

【目的】探明施用生物有机肥对菠萝心腐病的防控效果及对根际土壤微生物的影响。【方法】本研究采用高通量测序技术,综合分析不同施肥措施根际土壤微生物细菌群落多样性及群落特征。【结果】相比常规施肥处理(CK)和普通有机肥处理(YJ),生物有机肥处理KN (羊粪有机肥+泥炭土+枯草芽孢杆菌)和生物有机肥处理KY (羊粪有机肥+椰糠+枯草芽孢杆菌)均能显著降低菠萝心腐病的发病率,且KN处理的防控效果最佳。生物有机肥(KN、KY)施入后土壤细菌α多样性指数高于CK和YJ处理,并形成了明显不同的细菌群落结构。与CK相比,生物有机肥KN处理显著提高了拟杆菌门(Bacteroidetes)和厚壁菌门(Firmicutes)的丰度,KY处理中的酸杆菌门(Acidobacteria)、绿弯菌门(Chloroflexi)、芽单胞菌门(Gemmatimonadetes)、硝化螺旋菌门(Nitrospirae)丰度显著增加;属水平上,生物有机肥中的蔗糖伯克霍尔德菌属(Paraburkholderia)和黄杆菌属(Flavobacterium)丰度均显著提升。方差分区分析(variance partitioning analysis, VPA)表明,土壤化学性质(36.29%)对细菌群落影响最大,其中土壤速效钾和有机质是影响土壤细菌群落的关键因子,此外发病率(22.53%)和肥料偏生产力(16.42%)也是影响土壤细菌群落的重要因子。【结论】施用生物有机肥(KN、KY)能改变根际土壤细菌群落结构,降低发病率,对菠萝根际土壤生态系统稳定与健康具有重要意义。     

朱鹮肠道微生物多样性与产酶活性

【背景】朱鹮是我国国家一级保护动物,属于世界上最濒危的鸟类之一。对朱鹮肠道微生物的多样性和产胞外酶活性进行分析,可为朱鹮种群数量恢复提供思路。【目的】了解朱鹮肠道微生物的多样性,测定其产胞外酶活性。【方法】采用纯培养的方法获得朱鹮肠道微生物,通过革兰氏染色和生理生化鉴定,结合16S rRNA基因扩增和序列分析对细菌进行鉴定。使用水解圈法筛选产淀粉酶、蛋白酶、纤维素酶、脂肪酶的菌株。【结果】从人工喂养的朱鹮新鲜粪便中共分离到296株细菌,共计2个门11个属。变形菌门(Proteobacteria) 236株,占分离总数的79.73%,分别为：埃希氏菌属(Escherichia) 137株,占分离总数的46.28%;哈夫尼亚菌属(Hafnia) 39株,占分离总数的13.18%;变形菌属(Proteus) 28株,占分离总数的9.46%;柠檬酸杆菌属(Citrobacter) 23株,占分离总数的7.77%;气单胞菌属(Aeromonas) 6株,占分离总数的2.03%;肠杆菌属(Enterobacter) 1株,占分离总数的0.34%;志贺菌属(Shigella) 1株,占分离总数的0.34%;克雷伯菌属(Klebsiella) 1株,占分离总数的0.34%。厚壁菌门(Firmicutes) 60株,占分离总数的20.27%,分别为：肠球菌属(Enterococcus) 33株,占分离总数的11.15%;库特氏菌属(Kurthia) 14株,占分离总数的4.73%;芽孢杆菌属(Bacillus) 13株,占分离总数的4.39%。优势菌群为变形菌门(Proteobacteria)中的埃希氏菌属(Escherichia),占细菌总数的46.28%。经过生理生化鉴定,每个菌株生理生化鉴定出的种属与各自的16S rRNA基因鉴定出的种属相一致。产酶活力分析结果显示有238株产蛋白酶、25株产脂肪酶、24株产淀粉酶、15株产纤维素酶,分别占分离总数的80.41%、8.45%、8.11%和5.07%。【结论】朱鹮肠道微生物分离出的细菌可分为2门11属,优势菌群为变形菌门(Proteobacteria)中的埃希氏菌属(Escherichia),占细菌总数的46.28%;产酶活性分析显示,80.41%的菌株具有产蛋白酶能力。     

宁夏地区春季奶牛场牛舍土壤细菌群落特征

【背景】现代规模化生产模式下,牛舍环境管理是影响奶牛高效健康生产的重要因素。【目的】探讨牛场不同牛舍土壤细菌群落特征,为奶牛健康生产提供理论依据。【方法】采集宁夏某规模化奶牛场的哺乳犊牛岛、断奶犊牛舍、育成牛舍、低产泌乳牛舍、高产头胎泌乳牛舍、高产经产泌乳牛舍、干奶牛舍和病牛舍这8个不同牛舍的土样,每个牛舍6个重复,共48份土样。利用16S rRNA基因扩增子测序分析细菌群落结构与多样性,并对细菌群落的功能进行预测。【结果】不同牛舍土样细菌群落组成存在差异,并且8个牛舍中高产头胎泌乳牛舍土样的细菌群落多样性最高。哺乳犊牛岛土壤与其他牛舍土壤细菌群落在门水平上差异较大;泌乳期牛舍土样之间的细菌群落结构相似度较高。在门的水平上,拟杆菌门(Bacteroidetes)、变形菌门(Proteobacteria)、放线菌门(Actinobacteria)和厚壁菌门(Firmicutes)是这8个牛舍土样共有的优势菌门。在属的水平上,嗜盐碱的盐单胞菌属(Halomonas)、具有潜在降解特性的Fermentimonas和栖海面菌属(Aequorivita)及致病菌的鸟杆菌属(Ornithobacterium)是犊牛期牛舍土样的优势菌属;嗜盐碱的Truepera是育成牛舍土样的优势菌属;致病菌的不动杆菌属(Acinetobacter)和Parapedobacter、耐药菌的Pedobacter是泌乳期牛舍土样的优势菌属。【结论】致病菌和参与硝酸盐呼吸的细菌主要分布在哺乳犊牛岛,嗜盐碱菌主要分布在断奶犊牛舍和育成牛舍,产甲烷的细菌主要分布在高产头胎泌乳牛舍。本研究分析了不同牛舍土壤细菌群落多样性,为奶牛健康生产提供理论依据。     

焦化废水O/H/O生物处理工艺二级好氧生物反应器的微生物结构和功能

【背景】焦化废水O/H/O生物处理工艺的二级好氧生物反应器O₂具有剩余污染物矿化和完全硝化功能,对废水的达标排放有重要作用。【目的】阐明O₂生物反应器的微生物结构和功能。【方法】利用16S rRNA基因测序,研究O₂生物反应器的微生物多样性和组成并进行功能预测,揭示其共现性特征和环境影响因子。【结果】O₂的优势菌门以变形菌门(Proteobacteria)、拟杆菌门(Bacteroidetes)、绿菌门(Chlorobi)为主。主要菌属中红游动菌属(Rhodoplanes)、溶杆菌属(Lysobacter)、硫杆菌属(Thiobacillus)等参与化学需氧量(chemical oxygen demand,COD)、酚类(phenols)和硫氰酸盐(thiocyanate,SCN^-)等剩余污染物的去除,亚硝化弧菌属(Nitrosovibrio)和硝化螺菌属(Nitrospira)分别作为氨氧化细菌(ammonia-oxidizing bacteria,AOB)和主要的亚硝酸盐氧化细菌(nitrite-oxidizing bacteria,NOB)。功能预测结果显示苯甲酸酯降解、氨基苯甲酸酯降解、氯烷烃和氯烯烃的降解、氟代苯甲酸酯降解和硝基甲苯降解是外源物质生物降解和代谢的前五大通路,广泛分布在主要菌属中,验证了微生物降解剩余污染物的作用。基因pmoA/B/C-amoA/B/C、hao和nxrA/B编码相关的酶,组成了完整的硝化途径。共现网络结果揭示溶杆菌属、Candidatus Solibacter和红游动菌属在O₂生态中的重要地位。通过冗余分析(redundancy analysis,RDA)表明COD和NH₃是影响O₂微生物群落的主要因素。【结论】红游动菌属和溶杆菌属是O₂中最核心的功能菌属,在污染物矿化和维持群落生态稳定上有重要作用。亚硝化弧菌属和硝化螺菌属是硝化作用的核心菌属。O₂中的代谢通路以剩余污染物矿化和完全硝化为主,微生物群落主要受COD和NH₃的影响。本研究阐明了O₂的微生物结构与功能,为焦化废水O/H/O生物处理工艺的改进提供了微生物学上的依据。     

液固工艺山西陈醋发酵微生物群落组成、互作网络及溯源分析

【背景】传统山西陈醋是在开放环境下由多菌种固态发酵酿制而成,解析酿造过程中微生物群落的组成、互作网络及来源对认识和调控食醋发酵过程都具有重要意义。【目的】揭示山西陈醋酿造微生物群落的组成、演替、互作网络及来源。【方法】基于高通量测序技术揭示山西陈醋酿造过程中微生物群落的组成、演替和多样性;采用SPSS数据统计软件计算物种间的斯皮尔曼相关系数并利用Gephi软件对微生物群落互作网络进行可视化分析;采用快速期望最大化微生物源跟踪(fast expectation-maximization microbial source tracking, FEAST)方法解析发酵微生物群落的来源。【结果】山西陈醋酿造过程中有6个优势细菌属和5个优势真菌属(平均相对丰度大于1%);醋酸杆菌属(Acetobacter)、乳酸杆菌属(Lactobacillus)和复膜孢酵母属(Saccharomycopsis)的平均相对丰度较高,分别为20.76%、30.38%和46.24%;醋酸杆菌属(Acetobacter)的相对丰度在醋酸发酵阶段逐渐增加,而乳酸杆菌属(Lactobacillus)在此阶段的趋势则相反。微生物群落互作网络结果显示魏斯氏菌属(Weissella)、乳球菌属(Lactococcus)、季也蒙酵母属(Meyerozyma)、Loigolactobacillus、Schleiferilactobacillus和地杆菌属(Geobacter)具有较高的连接度(连接度≥7);此外,醋酸杆菌属(Acetobacter)与魏斯氏菌属(Weissella)、Schleiferilactobacillus、Loigolactobacillus、乳球菌属(Lactococcus)、季也蒙酵母属(Meyerozyma)具有显著的拮抗作用。来源追溯结果显示糖化发酵第2天样品中有1.02%的细菌群落和77.04%的真菌群落来源于大曲;在醋酸发酵第1天样品中有0.93%的细菌群落和52.82%的真菌群落来源于火醅。【结论】为了解山西陈醋酿造过程中微生物群落的组成、演替、互作网络和解释酿造微生物来源提供了重要的理论数据。     

不同耕作方式结合秸秆还田对玉米内生细菌多样性的影响

【目的】研究土默川平原不同耕作方式与秸秆还田模式下玉米内生细菌群落组成及功能,揭示不同耕作与秸秆还田方式促进玉米秸秆降解的内生菌资源,并为其选择性分离培养及其功能验证奠定基础。【方法】以内蒙古自治区土默川平原灌区连作玉米茎秆为研究对象,利用Illumina Miseq高通量测序技术,分析不同耕作及其秸秆还田方式连年定位试验条件下,玉米成熟期内生微生物多样性及群落结构差异。【结果】综合分析表明,免耕及深翻对玉米内生细菌群落多样性影响显著。不同耕作方式对玉米内生细菌群落组成结构的影响大于秸秆还田,玉米内生细菌群落结构首先可分为2类,第一类是免耕及其秸秆还田,第二类是其他7种耕作方式。从属水平来看,9种耕作方式共有的优势菌群分别为假单胞菌属(Pseudomonas)、肠杆菌科未分类属(unclassified_f__ Enterobacteriaceae)、泛菌属(Pantoea)、拉乌尔菌属(Raoultella)、拉恩氏菌属(Rahnella1),秸秆还田可增加拉乌尔菌属及肠杆菌科未分类属的丰度。【结论】不同耕作方式改变了玉米内生细菌多样性、群落组成和结构;秸秆还田处理能够增加玉米茎秆中对秸秆降解有积极作用的拉乌尔菌属及乳球菌属(Lactococcus)的相对丰度。     

Culture-dependent and culture-independent diversity of <Emphasis Type="Italic">Actinobacteria</Emphasis> associated with the marine sponge <Emphasis Type="Italic">Hymeniacidon perleve</Emphasis> from the South China Sea

In this report, the diversity of Actinobacteria associated with the marine sponge Hymeniacidon perleve collected from a remote island of the South China Sea was investigated employing classical cultivation and characterization, 16S rDNA library construction, 16S rDNA-restriction fragment length polymorphism (rDNA-RFLP) and phylogenetic analysis. A total of 184 strains were isolated using seven different media and 24 isolates were selected according to their morphological characteristics for phylogenetic analysis on the basis of their 16S rRNA gene sequences. Results showed that the 24 isolates were assigned to six genera including Salinispora, Gordonia, Mycobacterium, Nocardia, Rhodococcus and Streptomyces. This is the first report that Salinispora is present in a marine sponge from the South China Sea. Subsequently, 26 rDNA clones were selected from 191 clones in an Actinobacteria-specific 16S rDNA library of the H. perleve sample, using the RFLP technique for sequencing and phylogenetic analysis. In total, 26 phylotypes were clustered in eight known genera of Actinobacteria including Mycobacterium, Amycolatopsis, Arthrobacter, Brevibacterium, Microlunatus, Nocardioides, Pseudonocardia and Streptomyces. This study contributes to our understanding of actinobacterial diversity in the marine sponge H. perleve from the South China Sea.     

Diversity and abundance of ammonia-oxidizing prokaryotes in sediments from the coastal Pearl River estuary to the South China Sea

In the present study the diversity and abundance of nitrifying microbes including ammonia-oxidizing archaea (AOA) and betaproteobacteria (beta-AOB) were investigated, along with the physicochemical parameters potentially affecting them, in a transect of surface sediments from the coastal margin adjacent to the Pearl River estuary to the slope in the deep South China Sea. Nitrifying microbial diversity was determined by detecting the amoA (ammonia monooxygenase subunit A) gene. An obvious community structure shift for both AOA and beta-AOB from the coastal marginal areas to the slope in the deep-sea was detected, while the OTU numbers of AOA amoA were more stable than those of the beta-AOB. The OTUs of beta-AOB increased with the distance from the coastal margin areas to the slope in the deep-sea. Beta-AOB showed lower diversity with dominant strains in a polluted area but higher diversity without dominant strains in a clean area. Moreover, the diversity of beta-AOB was correlated with pH values, while no noticeable relationships were established between AOA and physicochemical parameters. Beta-AOB was more sensitive to transect environmental variability and might be a potential indicator for environmental changes. Additionally, the surface sediments surveyed in the South China Sea harboured diverse and distinct AOA and beta-AOB phylotypes different from other environments, suggesting the endemicity of some nitrifying prokaryotes in the South China Sea.     

Diverse Deep-Sea Fungi from the South China Sea and Their Antimicrobial Activity

We investigated the diversity of fungal communities in nine different deep-sea sediment samples of the South China Sea by culture-dependent methods followed by analysis of fungal internal transcribed spacer (ITS) sequences. Although 14 out of 27 identified species were reported in a previous study, 13 species were isolated from sediments of deep-sea environments for the first report. Moreover, these ITS sequences of six isolates shared 84–92 % similarity with their closest matches in GenBank, which suggested that they might be novel phylotypes of genera Ajellomyces, Podosordaria, Torula, and Xylaria. The antimicrobial activities of these fungal isolates were explored using a double-layer technique. A relatively high proportion (56 %) of fungal isolates exhibited antimicrobial activity against at least one pathogenic bacterium or fungus among four marine pathogenic microbes (Micrococcus luteus, Pseudoaltermonas piscida, Aspergerillus versicolor, and A. sydowii). Out of these antimicrobial fungi, the genera Arthrinium, Aspergillus, and Penicillium exhibited antibacterial and antifungal activities, while genus Aureobasidium displayed only antibacterial activity, and genera Acremonium, Cladosporium, Geomyces, and Phaeosphaeriopsis displayed only antifungal activity. To our knowledge, this is the first report to investigate the diversity and antimicrobial activity of culturable deep-sea-derived fungi in the South China Sea. These results suggest that diverse deep-sea fungi from the South China Sea are a potential source for antibiotics’ discovery and further increase the pool of fungi available for natural bioactive product screening.     

Seasonal and spatial diversity of microbial communities in marine sediments of the South China Sea

This study was conducted to characterize the diversity of microbial communities in marine sediments of the South China Sea by means of 16S rRNA gene clone libraries. The results revealed that the sediment samples collected in summer harboured a more diverse microbial community than that collected in winter, Deltaproteobacteria dominated 16S rRNA gene clone libraries from both seasons, followed by Gammaproteobacteria, Acidobacteria, Nitrospirae, Planctomycetes, Firmicutes. Archaea phylotypes were also found. The majority of clone sequences shared greatest similarity to uncultured organisms, mainly from hydrothermal sediments and cold seep sediments. In addition, the sedimentary microbial communities in the coastal sea appears to be much more diverse than that of the open sea. A spatial pattern in the sediment samples was observed that the sediment samples collected from the coastal sea and the open sea clustered separately, a novel microbial community dominated the open sea. The data indicate that changes in environmental conditions are accompanied by significant variations in diversity of microbial communities at the South China Sea.     

Conservation of reef corals in the South China Sea based on species and evolutionary diversity

The South China Sea in the Central Indo-Pacific is a large semi-enclosed marine region that supports an extraordinary diversity of coral reef organisms (including stony corals), which varies spatially across the region. While one-third of the world’s reef corals are known to face heightened extinction risk from global climate and local impacts, prospects for the coral fauna in the South China Sea region amidst these threats remain poorly understood. In this study, we analyse coral species richness, rarity, and phylogenetic diversity among 16 reef areas in the region to estimate changes in species and evolutionary diversity during projected anthropogenic extinctions. Our results show that richness, rarity, and phylogenetic diversity differ considerably among reef areas in the region, and that their outcomes following projected extinctions cannot be predicted by species diversity alone. Although relative rarity and threat levels are high in species-rich areas such as West Malaysia and the Philippines, areas with fewer species such as northern Vietnam and Paracel Islands stand to lose disproportionately large amounts of phylogenetic diversity. Our study quantifies various biodiversity components of each reef area to inform conservation planners and better direct sparse resources to areas where they are needed most. It also provides a critical biological foundation for targeting reefs that should be included in a regional network of marine protected areas in the South China Sea.     

中国南海部分深海沉积物真菌多样性及其抗菌活性

【目的】从南海4个站位的深海沉积物中分离真菌,揭示其多样性并测定抗菌活性。【方法】使用4种培养方法和8种培养基,从12个深海沉积物样本中分离培养真菌,通过菌落形态观察和ITS序列系统发育分析进行鉴定。采用滤纸片扩散法和生长速率法分别测试真菌小量发酵液粗浸膏的抗细菌和抗真菌活性。【结果】共分离到125株纯培养真菌,基于形态和ITS序列分析,排重后得到18个种类型,这些真菌可以划分到12个属,大多数属于子囊菌门(Ascomycota),只有2株属于担子菌门(Basidiomycota)。4个站位可培养真菌多样性具有差异性。抑菌活性筛选显示,大多数真菌具有较好的抑菌活性;链格孢属(Alternaria)、青霉属(Penicillium)、匐柄霉属(Stemphylium)这几个属的真菌表现出对多种指示细菌有抑制作用,尤其是Alternaria tenuissima DN09、Alternaria alternata DN14和Penicillium chrysogenum DN16对G~+和G~–细菌均表现出抑制作用。【结论】本研究揭示了南海深海沉积物可培养真菌多样性和抑菌活性,为进一步利用深海沉积物来源真菌奠定了基础。     

Phylogeography of Padina boryana (Dictyotales,Phaeophyceae) around the Thai-Malay Peninsula

The Indo-Pacific Ocean is a biodiversity hotspot for marine organisms. In this area, most of the research has focused on marine animals, such as reef fish, molluscs and other associated coral fauna, but very little has been done on macroalgae. The Thai-Malay Peninsula is an important north–south barrier in this area, which faces two different oceans – the Indian Ocean and the Pacific Ocean. This study aims to investigate genetic distribution patterns of Padina boryana Thivy around the Thai-Malay Peninsula, where it is common. Three DNA marker regions, the mitochondrion-encoded cytochrome c oxidase subunit 3 gene (cox3); the plastid rbcL, and the nuclear internal transcribed spacer 2 (ITS2) were used to evaluate genetic diversity and the relationships within and between populations. Samples were collected from both the Andaman Sea and Gulf of Thailand sides of the peninsula. Parsimony networks and maximum likelihood and Bayesian analyses showed clearly that there are two separated P. boryana lineages, one restricted to the Gulf of Thailand and the other to the Andaman Sea and other areas of the Indo-Pacific. The effect of different ocean currents along the Andaman Sea and Gulf of Thailand may have shaped these populations of P. boryana. This phylogeographic separation, based on persistent currents in the area, may affect other marine organisms along the Thai peninsula.     

Recovery and Phylogenetic Diversity of Culturable Fungi Associated with Marine Sponges <Emphasis Type="Italic">Clathrina luteoculcitella</Emphasis> and <Emphasis Type="Italic">Holoxea</Emphasis> sp. in the South China Sea

Sponge-associated fungi represent an important source of marine natural products, but little is known about the fungal diversity and the relationship of sponge–fungal association, especially no research on the fungal diversity in the South China Sea sponge has been reported. In this study, a total of 111 cultivable fungi strains were isolated from two South China Sea sponges Clathrina luteoculcitella and Holoxea sp. using eight different media. Thirty-two independent representatives were selected for analysis of phylogenetic diversity according to ARDRA and morphological characteristics. The culturable fungal communities consisted of at least 17 genera within ten taxonomic orders of two phyla (nine orders of the phylum Ascomycota and one order of the phylum Basidiomycota) including some potential novel marine fungi. Particularly, eight genera of Apiospora, Botryosphaeria, Davidiella, Didymocrea, Lentomitella, Marasmius, Pestalotiopsis, and Rhizomucor were isolated from sponge for the first time. Sponge C. luteoculcitella has greater culturable fungal diversity than sponge Holoxea sp. Five genera of Aspergillus, Davidiella, Fusarium, Paecilomyces, and Penicillium were isolated from both sponges, while 12 genera of Apiospora, Botryosphaeria, Candida, Marasmius, Cladosporium, Didymocrea, Hypocrea, Lentomitella, Nigrospora, Pestalotiopsis, Rhizomucor, and Scopulariopsis were isolated from sponge C. luteoculcitella only. Order Eurotiales especially genera Penicillium, Aspergillus, and order Hypocreales represented the dominant culturable fungi in these two South China Sea sponges. Nigrospora oryzae strain PF18 isolated from sponge C. luteoculcitella showed a strong and broad spectrum antimicrobial activities suggesting the potential for antimicrobial compounds production.     

Changhsingian brachiopod communities along a marine depth gradient in South China and their ecological significance in the end-Permian mass extinction

Diversity indices (dominance and evenness) and ecological spatial structure (lifestyles and relative abundances) are important features of Changhsingian brachiopod communities prior to the end-Permian mass extinction (EPME) and could predict temporal and spatial extinction patterns during the EPME. In South China, Changhsingian brachiopod communities show higher diversity than other contemporaneous brachiopod communities in the world and have been reported from a variety of sedimentary environments. In this paper, brachiopods from 18 sections in South China were selected to divide communities and compare their ecological structure. Based on the results of network analysis, cluster analysis and quantitative data from the selected sections, we show that Changhsingian brachiopod communities in South China can be categorized into three assemblages along a marine depth gradient: the Neochonetes–Fusichonetes–Paryphella Assemblage from the shallow-water clastic-rock facies, Spinomarginifera–Peltichia–Oldhamina Assemblage from the shallow-water carbonate platform facies and Fusichonetes–Crurithyris Assemblage from the deep-water siliciclastic intracontinental basin facies. Compared with communities from carbonate platform facies, the communities from siliciclastic facies were characterized by high dominance, low evenness and low lifestyle diversity, which might be important biotic factors leading to earlier extinctions. After the extinction began in all environments, the whole earliest Triassic brachiopod community was first dominated by Fusichonetes and then by Crurithyris. These patterns of domination and replacement could be explained by morphological and ecological advantages. The domination of these two genera, which were already adapted to the oxygen and food-limited deep-water habitat, indicates that the cooler deep-water environment might have been a relatively less stressed habitat after the beginning of the EPME. This suggests that global warming might be the main trigger among the previously proposed synergistic environmental stresses, while anoxia might not, at least for the beginning of EPME.     

Deep-Sea Biodiversity in the Mediterranean Sea: The Known,the Unknown,and the Unknowable

Deep-sea ecosystems represent the largest biome of the global biosphere, but knowledge of their biodiversity is still scant. The Mediterranean basin has been proposed as a hot spot of terrestrial and coastal marine biodiversity but has been supposed to be impoverished of deep-sea species richness. We summarized all available information on benthic biodiversity (Prokaryotes, Foraminifera, Meiofauna, Macrofauna, and Megafauna) in different deep-sea ecosystems of the Mediterranean Sea (200 to more than 4,000 m depth), including open slopes, deep basins, canyons, cold seeps, seamounts, deep-water corals and deep-hypersaline anoxic basins and analyzed overall longitudinal and bathymetric patterns. We show that in contrast to what was expected from the sharp decrease in organic carbon fluxes and reduced faunal abundance, the deep-sea biodiversity of both the eastern and the western basins of the Mediterranean Sea is similarly high. All of the biodiversity components, except Bacteria and Archaea, displayed a decreasing pattern with increasing water depth, but to a different extent for each component. Unlike patterns observed for faunal abundance, highest negative values of the slopes of the biodiversity patterns were observed for Meiofauna, followed by Macrofauna and Megafauna. Comparison of the biodiversity associated with open slopes, deep basins, canyons, and deep-water corals showed that the deep basins were the least diverse. Rarefaction curves allowed us to estimate the expected number of species for each benthic component in different bathymetric ranges. A large fraction of exclusive species was associated with each specific habitat or ecosystem. Thus, each deep-sea ecosystem contributes significantly to overall biodiversity. From theoretical extrapolations we estimate that the overall deep-sea Mediterranean biodiversity (excluding prokaryotes) reaches approximately 2805 species of which about 66% is still undiscovered. Among the biotic components investigated (Prokaryotes excluded), most of the unknown species are within the phylum Nematoda, followed by Foraminifera, but an important fraction of macrofaunal and megafaunal species also remains unknown. Data reported here provide new insights into the patterns of biodiversity in the deep-sea Mediterranean and new clues for future investigations aimed at identifying the factors controlling and threatening deep-sea biodiversity.