Psychrophiles
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EA41CH05-Cavicchioli ARI 30 April 2013 11:9 Psychrophiles Khawar S. Siddiqui,1 Timothy J. Williams,1 David Wilkins,1 Sheree Yau,1 Michelle A. Allen,1 Mark V. Brown,1,2 Federico M. Lauro,1 and Ricardo Cavicchioli1 1School of Biotechnology and Biomolecular Sciences and 2Evolution and Ecology Research Center, The University of New South Wales, Sydney, New South Wales 2052, Australia; email: [email protected] Annu. Rev. Earth Planet. Sci. 2013. 41:87–115 Keywords First published online as a Review in Advance on microbial cold adaptation, cold-active enzymes, metagenomics, microbial February 14, 2013 diversity, Antarctica The Annual Review of Earth and Planetary Sciences is online at earth.annualreviews.org Abstract This article’s doi: Psychrophilic (cold-adapted) microorganisms make a major contribution 10.1146/annurev-earth-040610-133514 to Earth’s biomass and perform critical roles in global biogeochemical cy- Copyright c 2013 by Annual Reviews. cles. The vast extent and environmental diversity of Earth’s cold biosphere All rights reserved has selected for equally diverse microbial assemblages that can include ar- Access provided by University of Nevada - Reno on 05/25/15. For personal use only. Annu. Rev. Earth Planet. Sci. 2013.41:87-115. Downloaded from www.annualreviews.org chaea, bacteria, eucarya, and viruses. Underpinning the important ecological roles of psychrophiles are exquisite mechanisms of physiological adaptation. Evolution has also selected for cold-active traits at the level of molecular adaptation, and enzymes from psychrophiles are characterized by specific structural, functional, and stability properties. These characteristics of en- zymes from psychrophiles not only manifest in efficient low-temperature activity, but also result in a flexible protein structure that enables biocatalysis in nonaqueous solvents. In this review, we examine the ecology of Antarctic psychrophiles, physiological adaptation of psychrophiles, and properties of cold-adapted proteins, and we provide a view of how these characteristics inform studies of astrobiology. 87 EA41CH05-Cavicchioli ARI 30 April 2013 11:9 INTRODUCTION Much of life on Earth has evolved to colonize low-temperature environments. In fact, at tem- peratures permanently below 5◦C, the cold biosphere represents by far the largest fraction of the global biosphere (Feller & Gerday 2003, Cavicchioli 2006, Siddiqui & Cavicchioli 2006, Casanueva et al. 2010, Margesin & Miteva 2011). Consistent with representative size, the cold biosphere consists of diverse types of environments—vast tracts of the deep sea, geographically dis- persed alpine regions, geologically specific subterranean caverns, climatically challenged regions of permafrost, and biogeochemically diverse polar reaches (Figure 1). Proliferating throughout these cold realms is a plethora of psychrophilic (cold-adapted) microorganisms—archaea, bacte- ria, eucarya, and viruses. A small proportion of the isolated microorganisms from naturally cold environments have a restricted growth temperature range with an upper growth temperature limit less than ∼20◦C (stenopsychrophile), whereas the majority of isolates have a broader temperature range, tolerating warmer temperatures (eurypsychrophile). Particularly through the application of molecular genetics approaches, most notably small sub- unit ribosomal RNA (SSU rRNA) sequencing, fluorescent in situ hybridization (FISH), and DNA sequencing of whole environmental samples (metagenomics), the cold biosphere has been discov- ered to harbor a diverse range of microbial groups. In recent years, the application of metagenomics and associated meta-functional approaches (metaproteomics and metatranscriptomics) has shed light on whole microbial community composition dynamics and microbial processes that are be- ing driven by the resident psychrophiles. Genomic, physiological, and biochemical analyses of psychrophilic isolates and their cellular components have also gleaned valuable information about the diverse molecular mechanisms of cold adaptation. As a result, whether driven by global ques- tions concerning the impact of ecosystem change on microbial communities in cold environments, fundamental studies of molecular structure and function, or biotechnologically driven pursuits of novel cold-active biocatalysts, the field of psychrophiles has made great advances. This review aims to cover topics relevant to studies of earth and planetary sciences by providing knowledge about physiological and protein adaptation—characteristics that speak to fundamental principles of biological adaptation to the cold and provide insight into survivability. A perspective on microbial ecology of Antarctic systems opens the review, particularly focusing on lake, sea-ice, and deep-sea environments—systems that include a broad range of physicochemical conditions Polar Alpine Extraterrestrial < 10°C e.g. Deep Lake, Deep sea e.g. Europa Access provided by University of Nevada - Reno on 05/25/15. For personal use only. Annu. Rev. Earth Planet. Sci. 2013.41:87-115. Downloaded from www.annualreviews.org Antarctica 1 to 4°C Surface: –200 to –160ºC –20°C Subsurface ocean: ?ºC Figure 1 Terrestrial and extraterrestrial cold environments. Representative temperatures are shown. 88 Siddiqui et al. EA41CH05-Cavicchioli ARI 30 April 2013 11:9 that provide knowledge about the diversity of microbial life that is sustained under a range of cold and abiotically varied environmental extremes. Also provided is a brief perspective on psychrophiles and global warming, providing a glimpse into the use of cold-active enzymes and its impact on psychrophiles in relation to climate change. The review concludes with a section reflecting on microbial extremes and cold-active enzymes and their relevance to astrobiology. ANTARCTIC PSYCHROPHILES Antarctic Aquatic Ecosystems Both southern and northern polar regions are delicately balanced ecosystems that are easily affected by ecosystem changes (Moline et al. 2004, Murray & Grzymski 2007, Wilkins et al. 2012b), and global warming is expected to cause changes that will flow through to organisms right up the food chain (Kirchman et al. 2009). In the Antarctic, global warming has particularly impacted the Antarctic Peninsula and West Antarctica (Meredith & King 2005, Murray & Grzymski 2007, Cavalieri & Parkinson 2008, Whitehouse et al. 2008, Reid et al. 2009, Steig et al. 2009, Hogg et al. 2011), and Antarctic sea-ice extent has decreased by at least ∼20% since the early 1950s and is projected to continue to decrease (Curran et al. 2003, Liu & Curry 2010). Ocean acidification (Kintisch & Stoksta 2008, McNeil & Matear 2008, Falkowski 2012), reduced CO2 absorption (Le Quer´ e´ et al. 2007), and reduced nutrient supply particularly at higher latitudes caused by increased stratification (Sarmiento & Le Quer´ e´ 1996, Wignall & Twitchett 1996, Matear & Hirst 1999) are all effects linked to global warming. As the ocean microorganisms are critical for sequestering anthropogenic CO2 (Sabine et al. 2004, Mikaloff Fletcher et al. 2006) and transporting it to the benthic zones (Thomalla et al. 2011), the changes taking place in polar waters are of great concern for the health of the global ecosystem. Even though only 50,850 km2 (0.4%) of Antarctica is seasonally ice free (Poland et al. 2003, Cary et al. 2010), a broad range of lake systems are distributed around Antarctica that maintain ice, water column, sediment, and microbial mat communities (Wilkins et al. 2012b). These lakes include subglacial, epiglacial, and surface systems that range in salinity from fresh to saturated and from mixed to permanently stratified. The evolutionary history of these lakes is as varied as the lakes themselves, which include the hundreds of marine-derived systems in the Vestfold Hills, which were isolated ∼3,000–7,000 years ago from the ocean (Gibson 1999) (Figure 2); subglacial outflow from Blood Falls dating from 1.5 Mya (Mikucki et al. 2009); and waters in the depths of subglacial Lake Vostok, which are probably even older (Siegert et al. 2001). Antarctic Microorganisms Colonize Diverse Cold Niches Microbial populations vary in accordance with the wide range of physical and chemical properties Access provided by University of Nevada - Reno on 05/25/15. For personal use only. Annu. Rev. Earth Planet. Sci. 2013.41:87-115. Downloaded from www.annualreviews.org of Antarctic lakes. In some marine-derived lakes, such as Ace Lake, the marine origin and, possibly, subsequent seeding from marine waters can be seen in the community composition of some parts of the water column (Lauro et al. 2011b) (Figure 2). However, this stratified system harbors vastly different communities in other parts of the lake where very different physicochemical conditions exist (Lauro et al. 2011b), including a highly purified population of green sulfur bacteria at the lake’s oxycline interface (Ng et al. 2010). The microbial communities in Lake Bonney have evolved in response to physical distinctions occurring in two different lobes of the lake (Glatz et al. 2006). Both of these examples illustrate how seed populations have diverged in response to ecosystem changes. The transition from a marine to a hypersaline environment at Deep Lake provides an extreme example of ecosystem change (Figure 2). Situated in the Vestfold Hills, Deep Lake is ∼55 m below sea level, 36 m deep, hypersaline (3.6–4.8 M), ice free, and perennially cold (e.g., −20◦C) (Ferris & Burton 1988, Franzmann et al. 1988). The system appears on the border of sustaining life;