{"id":2152,"date":"2016-01-21T00:37:45","date_gmt":"2016-01-21T00:37:45","guid":{"rendered":"http:\/\/192.168.99.100:8080\/research-activities\/research-themes\/"},"modified":"2020-07-31T17:48:10","modified_gmt":"2020-08-01T00:48:10","slug":"research-themes","status":"publish","type":"page","link":"https:\/\/www.darkenergybiosphere.org\/research-activities\/research-themes\/","title":{"rendered":"Research Themes"},"content":{"rendered":"<section class=\"l-section wpb_row height_medium\"><div class=\"l-section-h i-cf\"><div class=\"g-cols vc_row type_default valign_top\"><div class=\"vc_col-sm-12 wpb_column vc_column_container\"><div class=\"vc_column-inner\"><div class=\"wpb_wrapper\"><div class=\"wpb_text_column\" ><div class=\"wpb_wrapper\"><p>C-DEBI researchers are\u00a0conducting multi-disciplinary studies to develop an integrated understanding of subseafloor microbial life at the molecular, cellular, and ecosystem scales.\u00a0We will create knowledge of those traits of microbial life that are distinctive to the subseafloor environment, and address fundamental questions such as:<\/p>\n<ul>\n<li>What are the key sources and minimum fluxes of metabolic energy to support and maintain subseafloor life?<\/li>\n<li>What are the principles that govern physical, chemical, and biological interactions in ecosystems that experience long-term isolation or minimal connectivity?<\/li>\n<li>What are the molecular and physiological features of slow-growing microorganisms and how do they coordinate their metabolisms?<\/li>\n<\/ul>\n<p>Answers to these questions will provide, for the first time, a foundational understanding of the molecular and physiological features of subseafloor life, using the following themes as a framework:<\/p>\n<p><strong>Theme 1: <em>Fluxes, Connectivity, and Energy<\/em><\/strong> centers on subseafloor environmental conditions. We will quantify transfers of fluid, heat, solutes, carbon, and microbes within and between subseafloor biomes, and between the subseafloor and the overlying ocean; determine the nature of energy sources available to microbes in these ecosystems; and develop the next generation of coupled fluid-energy-biochemical-microbial models.<\/p>\n<p><strong>Theme 2: <em>Activities, Communities, and Ecosystems<\/em><\/strong> emphasizes resident microbial communities. We aim to illuminate the composition of subseafloor microbial communities and the functional potential of these communities, based on the diversity of metabolic activities and interactions with the physicochemical aspects of the system.<\/p>\n<p><strong>Theme 3: <em>Metabolism, Survival, and Adaptation<\/em><\/strong> concentrates on the actions and traits of individual microbial species. We will build a \u2018portfolio\u2019 of selected model subseafloor organisms and characterize their physiological and genetic traits. These microorganisms will be used to investigate energy and carbon use for growth and maintenance under kinetically limiting conditions and to determine rates of metabolism under specific conditions.<\/p>\n<p>Our three themes are highly complementary and intimately coupled. For example, fluxes of solutes and available energy sources (Theme 1) will inform on potential metabolic activities (Theme 2), which will be targeted in controlled laboratory experiments with model organisms (Theme 3), with the resulting data serving as input parameters for coupled models of subseafloor ecosystems (back to Theme 1). While feedback loops between themes are evident throughout, the order in which the themes are presented is not arbitrary; the founding constraints for microbial life in subseafloor environments are the underlying physical and chemical processes (Theme 1) within which microbial communities persist and build ecosystems (Theme 2), where individual microbial cells exhibit physiological and genetic traits characteristic for life at low energy fluxes and low growth rates (Theme 3).<\/p>\n<h2>Theme 1: Fluxes, Connectivity, and Energy<\/h2>\n<p><em>\u2014 centering on subseafloor environmental conditions<\/em><\/p>\n<\/div><\/div><div class=\"g-cols wpb_row  type_default valign_top vc_inner figure\"><div class=\"vc_col-sm-12 wpb_column vc_column_container\"><div class=\"vc_column-inner\"><div class=\"wpb_wrapper\"><div class=\"w-image align_none\"><a href=\"https:\/\/www.darkenergybiosphere.org\/wp-content\/uploads\/2016\/01\/theme1b.png\" ref=\"magnificPopup\" aria-label=\"Link\" class=\"w-image-h\"><img width=\"600\" height=\"370\" src=\"https:\/\/www.darkenergybiosphere.org\/wp-content\/uploads\/2016\/01\/theme1b.png\" class=\"attachment-us_600_0 size-us_600_0\" alt=\"\" loading=\"lazy\" srcset=\"https:\/\/www.darkenergybiosphere.org\/wp-content\/uploads\/2016\/01\/theme1b.png 1387w, https:\/\/www.darkenergybiosphere.org\/wp-content\/uploads\/2016\/01\/theme1b-300x185.png 300w, https:\/\/www.darkenergybiosphere.org\/wp-content\/uploads\/2016\/01\/theme1b-768x473.png 768w, https:\/\/www.darkenergybiosphere.org\/wp-content\/uploads\/2016\/01\/theme1b-1024x631.png 1024w, https:\/\/www.darkenergybiosphere.org\/wp-content\/uploads\/2016\/01\/theme1b-1200x740.png 1200w, https:\/\/www.darkenergybiosphere.org\/wp-content\/uploads\/2016\/01\/theme1b-200x123.png 200w, https:\/\/www.darkenergybiosphere.org\/wp-content\/uploads\/2016\/01\/theme1b-100x62.png 100w\" sizes=\"(max-width: 600px) 100vw, 600px\" \/><\/a><\/div><\/div><\/div><\/div><\/div><div class=\"wpb_text_column\" ><div class=\"wpb_wrapper\"><p>In Phase 1, C-DEBI researchers described the hydrologic, geochemical, and microbial connectivity within the crust on a kilometer scale; quantified the transfer and fate of solutes between the ocean, sediment, and subseafloor basalt; and located and sampled the first known site of massive, low-temperature hydrothermal discharge on a ridge flank. C-DEBI researchers were also the first to quantify energy yields of metabolic reactions and redox fluxes in deep sediment. In Phase 2, we will build on these achievements and focus on processes that control the movement of mass, heat, solutes, genetic material, and microbial cells within the deep subseafloor, and between this realm and the overlying ocean. We will also investigate the composition and distribution of electron acceptors, electron donors, and organic matter at new sites to evaluate <em>in situ<\/em> geochemical energy sources for microbial metabolism. Studies will test interpretations and hypotheses put forth in Phase 1 that often relied on sparse data. This scaling up by expanding existing and integrating new datasets, will allow us to generate regional and global maps and models of the subseafloor geochemistry and hydrology, and place potential microbial metabolisms in a broader context. Key research components in Theme 1 include multidisciplinary exploration, collection of field data, metabolic energy calculations, and coupled modeling of linked conditions and fluxes. The overarching Research Objectives in this theme are to:<\/p>\n<table>\n<tbody>\n<tr>\n<td style=\"text-align: left;vertical-align: top\"><strong>(1.1)\u00a0<\/strong><\/td>\n<td style=\"text-align: left;vertical-align: top\">Constrain the extent, variability, and controls on fluxes and connectivity within subseafloor biomes and between the subseafloor and the overlying ocean<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;vertical-align: top\"><strong>(1.2)\u00a0<\/strong><\/td>\n<td style=\"text-align: left;vertical-align: top\">Map the geochemical energy sources in subseafloor ecosystems at a range of spatial scales<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;vertical-align: top\"><strong>(1.3)\u00a0<\/strong><\/td>\n<td style=\"text-align: left;vertical-align: top\">Develop and test the next generation of coupled geochemical-hydrological-microbial models for subseafloor ecosystems<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h2>Theme 2: Communities, Activities, and Ecosystems<\/h2>\n<p><em>\u2014 emphasizing resident microbial communities<\/em><\/p>\n<\/div><\/div><div class=\"g-cols wpb_row  type_default valign_top vc_inner\"><div class=\"vc_col-sm-12 wpb_column vc_column_container\"><div class=\"vc_column-inner\"><div class=\"wpb_wrapper\"><div class=\"w-image align_none\"><a href=\"https:\/\/www.darkenergybiosphere.org\/wp-content\/uploads\/2016\/01\/theme2b.png\" ref=\"magnificPopup\" aria-label=\"Link\" class=\"w-image-h\"><img width=\"600\" height=\"634\" src=\"https:\/\/www.darkenergybiosphere.org\/wp-content\/uploads\/2016\/01\/theme2b.png\" class=\"attachment-us_600_0 size-us_600_0\" alt=\"\" loading=\"lazy\" srcset=\"https:\/\/www.darkenergybiosphere.org\/wp-content\/uploads\/2016\/01\/theme2b.png 1035w, https:\/\/www.darkenergybiosphere.org\/wp-content\/uploads\/2016\/01\/theme2b-284x300.png 284w, https:\/\/www.darkenergybiosphere.org\/wp-content\/uploads\/2016\/01\/theme2b-768x811.png 768w, https:\/\/www.darkenergybiosphere.org\/wp-content\/uploads\/2016\/01\/theme2b-970x1024.png 970w, https:\/\/www.darkenergybiosphere.org\/wp-content\/uploads\/2016\/01\/theme2b-200x211.png 200w, https:\/\/www.darkenergybiosphere.org\/wp-content\/uploads\/2016\/01\/theme2b-100x106.png 100w\" sizes=\"(max-width: 600px) 100vw, 600px\" \/><\/a><\/div><\/div><\/div><\/div><\/div><div class=\"wpb_text_column\" ><div class=\"wpb_wrapper\"><p>In Phase 1, C-DEBI researchers a) determined microbial community composition in samples from several subseafloor environments, b) undertook some of the first studies of metabolic potential in subseafloor ecosystems, c) carried out the first transcriptomic study of a subseafloor ecosystem, and d) quantified energy yields of metabolic reactions and redox fluxes in deep subseafloor systems. In Phase 2, we will build on these results to understand community structure and its drivers in subseafloor ecosystems. We will document the genetic composition of subseafloor communities and investigate functional potential and microbial activities to understand how energy and nutrients are transformed in subseafloor environments. Lastly, we will integrate these studies of community composition and microbial activities to test hypotheses of natural selection in the subseafloor. Field work, <em>in situ<\/em> activity measurements, stable isotope probing, and various &#8220;omics&#8221; approaches will take center stage, with these main research objectives:<\/p>\n<table>\n<tbody>\n<tr>\n<td style=\"text-align: left;vertical-align: top\"><strong>(2.1)\u00a0<\/strong><\/td>\n<td style=\"text-align: left;vertical-align: top\">Determine community composition, functional potential, and patterns of natural selection in subseafloor ecosystems<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;vertical-align: top\"><strong>(2.2)\u00a0<\/strong><\/td>\n<td style=\"text-align: left;vertical-align: top\">Determine metabolic activity of subseafloor microbial communities<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;vertical-align: top\"><strong>(2.3)\u00a0<\/strong><\/td>\n<td style=\"text-align: left;vertical-align: top\">Advance understanding of subseafloor microbe-virus interactions<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h2>Theme 3: Metabolism, Survival, and Adaptation<\/h2>\n<p><em><em>\u2014<\/em> concentrating on the actions and traits of individual microbial species<\/em><\/p>\n<\/div><\/div><div class=\"g-cols wpb_row  type_default valign_top vc_inner figure\"><div class=\"vc_col-sm-12 wpb_column vc_column_container\"><div class=\"vc_column-inner\"><div class=\"wpb_wrapper\"><div class=\"w-image align_none\"><a href=\"https:\/\/www.darkenergybiosphere.org\/wp-content\/uploads\/2016\/01\/theme3b.png\" ref=\"magnificPopup\" aria-label=\"Link\" class=\"w-image-h\"><img width=\"600\" height=\"498\" src=\"https:\/\/www.darkenergybiosphere.org\/wp-content\/uploads\/2016\/01\/theme3b.png\" class=\"attachment-us_600_0 size-us_600_0\" alt=\"\" loading=\"lazy\" srcset=\"https:\/\/www.darkenergybiosphere.org\/wp-content\/uploads\/2016\/01\/theme3b.png 1225w, https:\/\/www.darkenergybiosphere.org\/wp-content\/uploads\/2016\/01\/theme3b-300x249.png 300w, https:\/\/www.darkenergybiosphere.org\/wp-content\/uploads\/2016\/01\/theme3b-768x637.png 768w, https:\/\/www.darkenergybiosphere.org\/wp-content\/uploads\/2016\/01\/theme3b-1024x849.png 1024w, https:\/\/www.darkenergybiosphere.org\/wp-content\/uploads\/2016\/01\/theme3b-1200x995.png 1200w, https:\/\/www.darkenergybiosphere.org\/wp-content\/uploads\/2016\/01\/theme3b-200x166.png 200w, https:\/\/www.darkenergybiosphere.org\/wp-content\/uploads\/2016\/01\/theme3b-100x83.png 100w\" sizes=\"(max-width: 600px) 100vw, 600px\" \/><\/a><\/div><\/div><\/div><\/div><\/div><div class=\"wpb_text_column\" ><div class=\"wpb_wrapper\"><p>Themes 1 and 2 focus on subseafloor ecosystems, but many of the unique properties of the resident biota can best be investigated in the laboratory with model organisms or consortia. Theme 3 is therefore directed at examining the potential physiological, metabolic, and survival strategies employed under subseafloor conditions, including low energy flux and low or zero growth rates. It is highly likely that subseafloor microorganisms harbor fundamental traits that differ significantly from those of their faster-growing, laboratory-adapted counterparts. Uncovering the biochemical and genetic bases of those differences will inform our understanding of fundamental physiological processes of subseafloor microbes. Specifically, we will use selected model organisms to begin testing hypotheses generated from our field and <em>in situ<\/em> observations. While we fully recognize the limitations of culture-based systems to replicate natural environments, data from laboratory systems that are modified to specifically investigate unique aspects of subseafloor microbial life can serve as useful proxies for specific physiological aspects of such microbes\u00a0<em>in situ<\/em>. An organism\u2019s metabolic capabilities in the laboratory guide and constrain our understanding of its ability to adapt to specific environmental conditions. Theme 3 builds on and complements the large and growing database of microbial community structure and metagenomic data from diverse subseafloor environments. By studying model subseafloor organisms in the laboratory, we expect to gain important, novel, and basic insights into physiological and metabolic features that are unique to microbes in the subseafloor. The overarching research objectives in this theme are to:<\/p>\n<table>\n<tbody>\n<tr>\n<td style=\"text-align: left;vertical-align: top\"><strong>(3.1)\u00a0<\/strong><\/td>\n<td style=\"text-align: left;vertical-align: top\">Isolate and characterize novel bacteria and archaea from diverse subseafloor habitats<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;vertical-align: top\"><strong>(3.2)\u00a0<\/strong><\/td>\n<td style=\"text-align: left;vertical-align: top\">Examine fundamental physiology of subseafloor microbes under conditions of low growth rates and low energy flux<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;vertical-align: top\"><strong>(3.3)\u00a0<\/strong><\/td>\n<td style=\"text-align: left;vertical-align: top\">Perform adaptive evolution and long-term survival experiments with subseafloor microbes to characterize molecular genetic signatures associated with particular phenotypes.<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<div class=\"callout\">\n<p>For more information about our Research Themes, see the\u00a0<a href=\"https:\/\/www.darkenergybiosphere.org\/wp-content\/uploads\/docs\/2014C-DEBI_RenewalProposal.pdf\">C-DEBI renewal proposal<\/a>\u00a0(PDF)<\/p>\n<\/div>\n<\/div><\/div><\/div><\/div><\/div><\/div><\/div><\/section>\n","protected":false},"excerpt":{"rendered":"C-DEBI researchers are\u00a0conducting multi-disciplinary studies to develop an integrated understanding of subseafloor microbial life at the molecular, cellular, and ecosystem scales.\u00a0We will create knowledge of those traits of microbial life that are distinctive to the subseafloor environment, and address fundamental questions such as: What are the key sources and minimum fluxes of metabolic energy to...","protected":false},"author":1,"featured_media":0,"parent":2406,"menu_order":5,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/pages\/2152"}],"collection":[{"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/comments?post=2152"}],"version-history":[{"count":26,"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/pages\/2152\/revisions"}],"predecessor-version":[{"id":15237,"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/pages\/2152\/revisions\/15237"}],"up":[{"embeddable":true,"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/pages\/2406"}],"wp:attachment":[{"href":"https:\/\/www.darkenergybiosphere.org\/wp-json\/wp\/v2\/media?parent=2152"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}