How are candidate phylum JS1 bacteria adapted for life in the deep sub-seafloor biosphere?

JS1 门候选细菌如何适应海底深处生物圈的生活？

• 批准号: NE/J011177/1
• 负责人: Andrew Weightman
• 金额: $ 49.78万
• 依托单位: CARDIFF UNIVERSITY
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2012
• 资助国家: 英国
• 起止时间: 2012 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FJ011177%2F1
• 关键词: How; candidate; phylum; JS1; bacteria

In the mid-1990s we discovered an unusual group of bacteria in sediment samples collected from about 200 metres below the Japan Sea. We could not grow them on conventional laboratory media, in liquid or on agar in Petri dishes, but they were identified by sequencing 16S rRNA genes directly from the sediment that allowed us to relate them to other established bacterial species. Further studies that we and others carried out showed that these bacteria were highly abundant in many parts of the deep sub-seafloor biosphere, and that they constituted a potential or candidate new division or phylum, which we called JS1. As microbiologists started to use DNA analysis more routinely to investigate bacteria, and microbial communities generally, it became apparent that the vast majority of bacterial species could not be grown in the lab. For example, in marine sediment 0.1% or less of species were uncultivated; candidate phylum JS1 bacteria was just one of 50, possibly 100 candidate phyla which had no cultivated representative and could only be identified on the basis of their 16S rRNA genes. If the phyla containing pathogens like Escherichia coli (Proteobacteria) and MRSA (Firmicutes), or the photosynthetic bacteria (Cyanobacteria), or the antibiotic-producing Actinobacteria were as poorly understood it is difficult to imagine what the consequences would have been for medicine, industry and society.This research aims to assemble a strong team of collaborating scientists, led by the Cardiff group who have pioneered developments in deep biosphere research over the last two decades. This collaboration provides a unique opportunity to exploit some recent research in Europe and the USA, developing methods for genome analysis using individual cells isolated by techniques such as fluorescence-activated cell sorting and microfluidic laser capture. Single cells of JS1 bacteria have been isolated by collaborators at Aarhus University, Denmark, and one of the first aims of the proposed project is to sequence their genomes. In parallel, our collaborators at UNLV, USA, will be working on a potentially related candidate phylum (OP9), single cells of which they have isolated from hot springs in Yellowstone Park. Another project partner at MIT, USA, has cloned JS1 genomic DNA fragments from an oil reservoir, and will collaborate with the Cardiff team to sequence these fragments. In addition to the single cell JS1 genome sequencing, we will be trying to improve cultivation of these bacteria from sediments in the laboratory, using a variety of systems including high-pressure cultivation. This part of the project will also involve developing DNA markers to investigate further the distribution and diversity of JS1 bacteria in sediments from across the Earth, many samples of which are already stored in an archive at -80oC at Cardiff. Methods to amplify DNA from low concentrations (QPCR) will be used to quantify JS1 bacteria in sub-surface sediment, and a method called CARD-FISH to visualize and count them, will be used in partnership with a collaborator at Hannover, Germany. Another aim of the project, therefore, is to obtain cultures in the lab that are highly enriched in JS1 bacteria, and to extract DNA and RNA from these cultures that can be sequenced and analysed for comparison to the single cell and cloned genomic DNA. However, interactions between JS1 bacteria and other microbes are likely to be very important in terms of their activities and biogeochemical cycles, so we will also want to learn about the community of bacteria and other microorganisms with which JS1 bacteria are associated.Thus, although we know JS1 bacteria are abundant and widespread in deep biosphere sediments across the globe (indeed they may constitute one of the most abundant taxa on Earth), we don't know much else about them. Ultimately, this project aims to answer the question: how are JS1 bacteria are adapted for life in the deep sub-seafloor biosphere?

20世纪90年代中期，我们在日本海下约200米的沉积物样本中发现了一组不同寻常的细菌。我们不能在常规的实验室培养基上、液体中或培养皿中的琼脂上培养它们，但它们是通过直接从沉淀物中测序16S rRNA基因来鉴定的，这使我们能够将它们与其他已建立的细菌物种联系起来。我们和其他人进行的进一步研究表明，这些细菌在深海海底生物圈的许多部分都高度丰富，它们构成了一个潜在或候选的新门或门，我们称之为JS1。随着微生物学家开始更常规地使用DNA分析来研究细菌和微生物群落，很明显，绝大多数细菌物种不能在实验室中培养。例如，在海洋沉积物中，0.1%或更少的物种是未培养的；候选门JS1细菌只是50个、可能100个候选门中的一个，这些候选门没有培养的代表性，只能根据它们的16S rRNA基因进行鉴定。如果对含有病原体的门，如大肠杆菌(变形杆菌)和MRSA(菲尔米库斯)，或光合作用细菌(蓝藻)，或产生抗生素的放线菌了解很少，很难想象这会对医学、工业和社会造成什么后果。这项研究旨在组建一个由卡迪夫小组领导的强大的合作科学家团队，他们在过去20年里开创了深层生物圈研究的先河。这一合作提供了一个独特的机会，可以利用欧洲和美国最近的一些研究，开发使用通过荧光激活细胞分选和微流控激光捕获等技术分离的单个细胞进行基因组分析的方法。丹麦奥胡斯大学的合作者已经分离出JS1细菌的单细胞，拟议项目的首要目标之一是对它们的基因组进行测序。与此同时，我们在美国UNLV的合作者将致力于一个可能相关的候选门(OP9)，他们已经从黄石公园的温泉中分离出了这种单细胞。美国麻省理工学院的另一个项目合作伙伴已经从一个储油罐中克隆了JS1基因组DNA片段，并将与加的夫团队合作对这些片段进行测序。除了单细胞JS1基因组测序外，我们还将努力改进实验室中从沉积物中培养这些细菌的方法，使用包括高压培养在内的各种系统。该项目的这一部分还将涉及开发DNA标记，以进一步调查地球各地沉积物中JS1细菌的分布和多样性，其中许多样本已经存储在加的夫-80摄氏度的档案馆中。从低浓度中扩增DNA的方法(QPCR)将用于量化地下沉积物中的JS1细菌，一种名为CARD-FISH的方法将用于对它们进行可视化和计数，该方法将与德国汉诺威的一个合作者合作使用。因此，该项目的另一个目标是在实验室获得高度富含JS1细菌的培养物，并从这些培养物中提取DNA和RNA，可以对其进行测序和分析，以便与单细胞和克隆的基因组DNA进行比较。然而，JS1细菌和其他微生物之间的相互作用在它们的活动和生物地球化学循环方面可能非常重要，所以我们还想了解与JS1细菌相关的细菌和其他微生物的群落。因此，尽管我们知道JS1细菌在全球生物圈深层沉积物中大量存在和广泛分布(事实上，它们可能构成地球上最丰富的类群之一)，但我们对它们知之甚少。最终，该项目旨在回答这个问题：JS1细菌是如何适应海底深处生物圈的生命的？

项目成果

Chronic effects of temperature and nitrate pollution on Daphnia magna: Is this cladoceran suitable for widespread use as a tertiary treatment?

温度和硝酸盐污染对大型溞的慢性影响：这种枝角动物是否适合广泛用作三级处理？

• DOI: 10.1016/j.watres.2015.06.036
• 发表时间: 2015
• 期刊: Water research
• 影响因子: 12.8
• 作者: Maceda-Veiga A

Rock-crushing derived hydrogen directly supports a methanogenic community: significance for the deep biosphere.

岩石破碎产生的氢直接支持产甲烷群落：对深层生物圈的意义。

• DOI: 10.1111/1758-2229.12723
• 发表时间: 2019
• 期刊: Environmental microbiology reports
• 影响因子: 3.3
• 作者: Parkes RJ

Changes in Metal Leachability through Stimulation of Iron Reducing Communities within Waste Sludge

通过刺激废污泥中的铁还原群来改变金属浸出率

• DOI: 10.4028/www.scientific.net/ssp.262.269
• 发表时间: 2017
• 期刊: Solid State Phenomena
• 作者: Roberts M

Survival of Desulfotomaculum spores from estuarine sediments after serial autoclaving and high-temperature exposure.

• DOI: 10.1038/ismej.2014.190
• 发表时间: 2015-03-17
• 期刊: The ISME journal
• 作者: O'Sullivan LA;Roussel EG;Weightman AJ;Webster G;Hubert CR;Bell E;Head I;Sass H;Parkes RJ
• 通讯作者: Parkes RJ

Contrasting relationships between biogeochemistry and prokaryotic diversity depth profiles along an estuarine sediment gradient.

• DOI: 10.1111/1574-6941.12106
• 发表时间: 2013-07
• 期刊: FEMS microbiology ecology
• 影响因子: 4.2
• 作者: Louise A. O’Sullivan;A. Sass;G. Webster;J. Fry;R. Parkes;A. Weightman