南大西洋深海热液区可培养硫氧化微生物多样性及其硫氧化特性

【目的】探索南大西洋热液环境中的硫氧化细菌多样性并研究其硫氧化特性。【方法】通过富集培养和分离纯化获得硫氧化细菌,利用变性梯度凝胶电泳(DGGE)分析富集菌群组成结构,采用离子色谱法对获得的硫氧化细菌硫氧化特性进行检测。【结果】从南大西洋深海环境样品中共分离到48株菌,分属于alpha-Proteobacteria(28株,58.3%)、Actinobacteria(11株,22.9%)和gama-Proteobacteria(9株,18.8%)共3个门,其中Thalassospira、Martelella和Microbacterium为优势属。DGGE结果表明深海热液环境样品中微生物多样性丰富且不同站位存在差异。硫氧化特性研究结果表明,约60%的分离菌株具有硫氧化能力,可以氧化S_2O_3~(2–)生成SO_4~(2–)。获得一株硫氧化能力较强的潜在新种L6M1-5,在实验条件下可高效氧化S_2O_3~(2–),最大氧化速率可达0.56 mmol/(L·h)。【结论】南大西洋深海热液环境中可培养硫氧化细菌多样性丰富,为研究热液环境中的硫循环过程提供了实验材料和理论参考;同时高效硫氧化菌的获得,为工业化含硫废水的处理提供了良好的菌种资源。     

冲绳海槽热液区可培养硫氧化细菌多样性及其硫氧化特性

冲绳海槽热液区独特的地质环境孕育了特殊的生物群落,硫氧化细菌作为生物地球化学循环的重要参与者在热液生态系统中发挥着至关重要的作用。【目的】通过硫氧化菌株的分离培养揭示冲绳海槽热液区可培养硫氧化细菌的多样性和硫氧化活性。【方法】采用多种培养基对冲绳海槽热液区不同沉积物样品中的硫氧化细菌进行富集培养和分离纯化;利用16S rRNA基因序列确定硫氧化细菌的分类地位并进行系统发育分析;采用碘量法对典型硫氧化菌株硫氧化活性进行检测。【结果】本研究从冲绳海槽热液区样品中共分离鉴定85株硫氧化细菌,分属于α-变形菌纲、γ-变形菌纲、放线菌门和厚壁菌门,优势属为氢弧菌属(Hydrogenovibrio)、拉布伦氏菌属(Labrenzia)、深海海旋菌属(Thalassospira)和海杆状菌属(Marinobacter)。硫氧化活性检测结果表明,7株典型硫氧化菌株对硫代硫酸钠的降解活性介于31%–100%之间,其中泰坦尼克号盐单胞菌SOB56 (Halomonas titanicae SOB56)、南极海杆状菌SOB93(Marinobacter antarcticus SOB93)、印度硫氧化粗杆菌SOB107 (Thioclava indica SOB107)和嗜温氢弧菌CJG136 (Hydrogenovibrio thermophiles CJG136)可以完全降解硫代硫酸钠。【结论】冲绳海槽热液区可培养硫氧化细菌的多样性丰富,为研究该热液区的硫循环过程提供了实验材料和理论基础,多种硫氧化活性菌株的获得极大地丰富了菌种资源,为探究深海热液区硫循环的能量代谢途径和分子机制奠定基础。     

硫氧化细菌的种类及硫氧化途径的研究进展

硫,作为生物必需的大量营养元素之一,参与了细胞的能量代谢与蛋白质、维生素和抗生素等物质代谢。自然界中,硫以多种化学形态存在,包括单质硫、还原性硫化物、硫酸盐和含硫有机物。硫氧化是硫元素生物地球化学循环的重要组成部分,通常是指单质硫或还原性硫化物被微生物氧化的过程。硫氧化细菌种类繁多,其硫氧化相关基因、酶和途径也多种多样。近几年,相关方面的研究已取得很多进展,但在不同层面仍存在一些尚未解决的科学问题。本文主要围绕硫氧化细菌的种类及硫氧化途径的研究进展进行了综述。     

嗜酸硫氧化细菌消解元素硫的研究进展

浸矿酸性环境下,金属硫化矿在Fe3+作用下,经过硫代硫酸盐途径或多聚硫化氢途径而分解的过程中导致大量元素硫的累积,进而可能在金属硫化矿表面形成疏水元素硫层,阻碍金属离子的进一步浸出。酸性环境下,惰性元素硫的消解必须借助嗜酸硫氧化细菌来实现。该消解过程包括嗜酸硫氧化细菌对元素硫的吸附、转运以及氧化转化等过程。本文对近年来嗜酸硫氧化细菌消解元素硫过程的相关研究进行了全面评述,认为有关嗜酸硫氧化细菌消解元素硫的分子机制的清晰阐述还有待人们通过对消解过程的各个环节的分子机制进行大量研究来实现。     

硫氧化细菌源单质硫的生成、转运和回收

单质硫(硫粒)是硫化物生物氧化的中间产物.按化学计量式精准调控O/S比(溶解氧与硫化物的摩尔比),单质硫可成为硫氧化细菌(Sulfur-oxidizing bacteria,SOB)的主要代谢产物.根据单质硫的分布,单质硫可分为胞内硫粒和胞外硫粒.单质硫由胞内向胞外的跨膜转运过程是泌硫型SOB的重要生理特征.从生物脱硫...     

湖泊硫循环微生物研究进展

湖泊是响应气候和环境变化的关键生态系统,是研究元素(如碳、氮和硫等)生物地球化学循环的热点环境。湖泊(尤其咸盐湖)具有硫酸盐含量高且含硫化合物种类丰富的特点,因而湖泊中硫元素生物地球化学循环过程非常活跃。微生物是驱动湖泊硫循环的重要推手。因此,研究湖泊中微生物参与的硫元素生物地球化学循环过程以及相关微生物类群构成,对于深入探索微生物在湖泊生态系统中的作用具有重要意义。本文综述了湖泊中驱动硫循环的微生物(硫氧化菌和硫酸盐还原菌)种群多样性、功能基因、代谢途径、硫氧化/硫酸盐还原速率及其对环境条件变化响应等方面的研究现状,并对未来湖泊微生物驱动的硫循环研究方向进行了展望。     

无机硫化合物的微生物氧化

无机硫化合物的微生物氧化徐海岩,颜望明（山东大学微生物研究所,济南２５０１００）硫是自然界存在的重要元素之一,也是构成生物有机体必不可少的一种元素。自然界硫的转化主要是在微生物直接或间接参与下完成的。在这些微生物中,有异养菌,也有自养菌。自养菌主要是...     

嗜热古菌异化型硫氧化途径的研究进展

微生物参与的还原性无机硫化合物的氧化过程是硫地球化学循环的重要组成部分,也可应用于生物冶金工业及酸性矿水治理等方面。嗜热古菌是高温环境中存在的一群特殊的微生物,其所参与的异化型硫氧化途径复杂多样,涉及众多氧化还原酶以及硫转运蛋白。本文将结合我们的研究工作,就参与异化型硫氧化代谢过程的嗜热古菌的种类,以及它们所参与的硫氧化过程进行系统的介绍。     

嗜酸硫杆菌属硫氧化系统研究进展

硫化矿的酸溶解和化学氧化过程中(H 和Fe3 作用下,金属硫化矿中分解),伴随着硫元素转变成多聚硫S8或硫代硫酸盐的过程。对嗜酸硫杆菌属硫氧化过程的研究表明,胞外环状多聚硫S8可能通过细胞外膜蛋白巯基活化成线状-SnH后,被转运到细胞周质区域,进而被硫加双氧酶氧化成SO32-,活化过程中同时生成少量H2S;这些酶促反应不需要辅助因子参与,不释放电子。胞外硫代硫酸盐通过未知途径进入细胞周质。细胞周质中的SO32-主要经由亚硫酸-受体氧化还原酶氧化成SO42-,S2O32-可能经由硫代硫酸盐-辅酶Q氧化还原酶、硫代硫酸盐脱氢酶、连四硫酸盐水解酶等氧化为硫酸,少量H2S则经由硫化物-辅酶Q氧化还原酶氧化为多聚硫,后者再经由SO32-和S2O32-氧化生成最后产物SO42-。这些生物氧化过程释放的电子进入呼吸链参与产生细菌生长代谢所需的能量。然而,关于A.ferrooxidans硫氧化系统中各种硫化合物的酶催化氧化机制的研究仍很缺乏,胞内外硫化合物的转运机制、是否存在胞外酶催化氧化等仍然有待解决。另外,硫的型态和价态、酶催化反应的细胞微区域以及硫氧化系统中一些关键酶的分离及其表达基因的鉴定等问题都还有待进一步研究。基于对这些事实的分析,提出了一个嗜酸硫杆菌属硫氧化系统的模型。     

微生物硫循环网络的研究进展

硫元素是所有生物的基本组成成分,是生物体必需的营养元素之一。硫氧化还原微生物的数量多、分布广、代谢途径多样化,硫化合物之间的平衡依赖于微生物代谢网络中的各种硫转化反应与代谢过程。此外,硫循环与碳、氮循环紧密相关,对地球生态循环起到了至关重要的作用。本文综述了近期微生物硫循环网络的研究进展,包括所涉及的主要微生物、硫循环的生物化学途径、硫循环的环境意义和工业应用潜能等,深入了解自然和人工生态系统中存在的硫循环过程,可为控制工农业生产中硫元素的增减与利用提供理论基础与应用方案。     

Chemolithotrophic Sulfur-Oxidizing Bacteria from the Galapagos Rift Hydrothermal Vents

Three distinct physiological types of sulfur-oxidizing bacteria were enriched and isolated from samples collected at several deep-sea hydrothermal vents (2,550 m) of the Galapagos Rift ocean floor spreading center. Twelve strains of the obligately chemolithotrophic genus Thiomicrospira were obtained from venting water and from microbial mats covering surfaces in the immediate vicinity of the vents. From these and other sources two types of obligately heterotrophic sulfur oxidizers were repeatedly isolated that presumably oxidized thiosulfate either to sulfate (acid producing; 9 strains) or to polythionates (base producing; 74 strains). The former were thiobacilli-like, exhibiting a thiosulfate-stimulated increase in growth and CO₂ incorporation, whereas the latter were similar to previously encountered pseudomonad-like heterotrophs. The presence of chemolithotrophic sulfur-oxidizing bacteria in the sulfide-containing hydrothermal water supports the hypothesis that chemosynthesis provides a substantial primary food source for the rich populations of invertebrates found in the immediate vicinity of the vents.     

Major contribution of sulfide-derived sulfur to the benthic food web in a large freshwater lake

In freshwater systems, contributions of chemosynthetic products by sulfur-oxidizing bacteria in sediments as nutritional resources in benthic food webs remain unclear, even though chemosynthetic products might be an important nutritional resource for benthic food webs in deep-sea hydrothermal vents and shallow marine systems. To study geochemical aspects of this trophic pathway, we sampled sediment cores and benthic animals at two sites (90 and 50 m water depths) in the largest freshwater (mesotrophic) lake in Japan: Lake Biwa. Stable carbon, nitrogen, and sulfur isotopes of the sediments and animals were measured to elucidate the sulfur nutritional resources for the benthic food web precisely by calculating the contributions of the incorporation of sulfide-derived sulfur to the biomass and of the biogeochemical sulfur cycle supporting the sulfur nutritional resource. The recovered sediment cores showed increases in ³⁴S-depleted sulfide at 5 cm sediment depth and showed low sulfide concentration with high δ³⁴S in deeper layers, suggesting an association of microbial activities with sulfate reduction and sulfide oxidation in the sediments. The sulfur-oxidizing bacteria may contribute to benthic animal biomass. Calculations based on the biomass, sulfur content, and contribution to sulfide-derived sulfur of each animal comprising the benthic food web revealed that 58%–67% of the total biomass sulfur in the benthic food web of Lake Biwa is occupied by sulfide-derived sulfur. Such a large contribution implies that the chemosynthetic products of sulfur-oxidizing bacteria are important nutritional resources supporting benthic food webs in the lake ecosystems, at least in terms of sulfur. The results present a new trophic pathway for sulfur that has been overlooked in lake ecosystems with low-sulfate concentrations.     

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。     

一株嗜酸硫杆菌M4-422-6的分离及其全基因组测序和比较基因组学分析

【目的】开展具有硫氧化能力的嗜酸硫杆菌属(Acidithiobacillus)的分离及其比较基因组学分析,不仅可以丰富硫氧化细菌菌种资源,而且有助于加深理解嗜酸硫杆菌的分子进化与生态适应机制。【方法】利用以硫代硫酸钠为唯一能源的培养基分离具有硫氧化能力的细菌;利用Illumina HiSeq X和Oxford Nanopore测序平台对一株嗜酸硫杆菌M4-422-6进行全基因组测序;利用相关生物信息学分析软件对原始数据进行组装和基因组注释,并与一株亲缘关系最近的菌株Igneacidithiobacillus copahuensis VAN18-1进行比较基因组学分析。【结果】分离获得一株具有硫氧化能力的嗜酸硫杆菌M4-422-6。基因组注释结果显示,菌株M4-422-6基因组由1个染色体和2个质粒组成,基因组大小为2 917 823 bp,G+C含量为58.54%,共编码2 925个蛋白。16S rRNA基因和基因组系统发育树显示,菌株M4-422-6代表嗜酸硫杆菌属的一个潜在新种。功能基因注释结果显示,菌株Acidithiobacillus sp. M4-422-6拥有与菌株特性相关的众多基因,包括硫氧化相关基因、CO₂固定相关基因和耐酸相关基因。比较基因组学分析发现,虽然菌株M4-422-6与VAN18-1的亲缘关系最近,但两者仍拥有众多的差异基因,主要包括噬菌体抗性相关基因和移动元件编码基因。【结论】菌株M4-422-6代表嗜酸硫杆菌属的一个潜在新种,该菌株具有同种内菌株所不具有的特有基因,并据此推测嗜酸硫杆菌种内分化可归因于对特定生态位的适应。     

The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2

Presented here is the complete genome sequence of Thiomicrospira crunogena XCL-2, representative of ubiquitous chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal vents. This gammaproteobacterium has a single chromosome (2,427,734 base pairs), and its genome illustrates many of the adaptations that have enabled it to thrive at vents globally. It has 14 methyl-accepting chemotaxis protein genes, including four that may assist in positioning it in the redoxcline. A relative abundance of coding sequences (CDSs) encoding regulatory proteins likely control the expression of genes encoding carboxysomes, multiple dissolved inorganic nitrogen and phosphate transporters, as well as a phosphonate operon, which provide this species with a variety of options for acquiring these substrates from the environment. Thiom. crunogena XCL-2 is unusual among obligate sulfur-oxidizing bacteria in relying on the Sox system for the oxidation of reduced sulfur compounds. The genome has characteristics consistent with an obligately chemolithoautotrophic lifestyle, including few transporters predicted to have organic allocrits, and Calvin-Benson-Bassham cycle CDSs scattered throughout the genome.     

The Genome of Deep-Sea Vent Chemolithoautotroph Thiomicrospira crunogena XCL-2

Presented here is the complete genome sequence of Thiomicrospira crunogena XCL-2, representative of ubiquitous chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal vents. This gammaproteobacterium has a single chromosome (2,427,734 base pairs), and its genome illustrates many of the adaptations that have enabled it to thrive at vents globally. It has 14 methyl-accepting chemotaxis protein genes, including four that may assist in positioning it in the redoxcline. A relative abundance of coding sequences (CDSs) encoding regulatory proteins likely control the expression of genes encoding carboxysomes, multiple dissolved inorganic nitrogen and phosphate transporters, as well as a phosphonate operon, which provide this species with a variety of options for acquiring these substrates from the environment. Thiom. crunogena XCL-2 is unusual among obligate sulfur-oxidizing bacteria in relying on the Sox system for the oxidation of reduced sulfur compounds. The genome has characteristics consistent with an obligately chemolithoautotrophic lifestyle, including few transporters predicted to have organic allocrits, and Calvin-Benson-Bassham cycle CDSs scattered throughout the genome.     

On the evolutionary ecology of symbioses between chemosynthetic bacteria and bivalves

Mutualistic associations between bacteria and eukaryotes occur ubiquitously in nature, forming the basis for key ecological and evolutionary innovations. Some of the most prominent examples of these symbioses are chemosynthetic bacteria and marine invertebrates living in the absence of sunlight at deep-sea hydrothermal vents and in sediments rich in reduced sulfur compounds. Here, chemosynthetic bacteria living in close association with their hosts convert CO₂ or CH₄ into organic compounds and provide the host with necessary nutrients. The dominant macrofauna of hydrothermal vent and cold seep ecosystems all depend on the metabolic activity of chemosynthetic bacteria, which accounts for almost all primary production in these complex ecosystems. Many of these enigmatic mutualistic associations are found within the molluscan class Bivalvia. Currently, chemosynthetic symbioses have been reported from five distinct bivalve families (Lucinidae, Mytilidae, Solemyidae, Thyasiridae, and Vesicomyidae). This brief review aims to provide an overview of the diverse physiological and genetic adaptations of symbiotic chemosynthetic bacteria and their bivalve hosts.