Biodiversity of poly-extremophilic Bacteria: Does combining the extremes of high salt, alkaline pH and elevated temperature approach a physico-chemical boundary for life?

Bacterial microorganisms that grow optimally at Na⁺ concentrations of 1.7 M, or the equivalent of 10% (w/v) NaCl, and greater are considered to be extreme halophiles. This review focuses on the correlation between the extent of alkaline pH and elevated temperature optima and the extent of salt tolerance of extremely halophilic eubacteria; the focus is on those with alkaline pH optima, above 8.5, and elevated temperature optima, above 50°C. If all three conditions are required for optimal growth, these microorganisms are termed "poly-extremophiles". However, only a very few extreme halophiles able to grow optimally under alkaline conditions as well as at elevated temperatures have been isolated so far. Therefore the question is: do the combined extreme growth conditions of the recently isolated poly-extremophiles, i.e., anaerobic halophilic alkalithermophiles, approach a physico-chemical boundary for life? These poly-extremophiles are of interest, as their adaptive mechanisms give insight into organisms' abilities to survive in environments which were previously considered prohibitive to life, as well as to possible properties of early evolutionary and extraterrestrial life forms.     

可培养盐碱菌多样性的研究进展

存在于高盐强碱极端环境的微生物因其独特的生命方式,引起了广泛的关注。根据盐碱环境所含的可溶性盐成分,可分为"NaCl型"和"苏打型(Na_2CO_3/NaHCO_3)"两大类,前者的碱性pH值较低而后者碱性pH值较高。本文总结了盐碱菌适宜生长条件在盐度0.5 mol/L和碱性pH 9.0之上且有效发表的标准菌株,并对这些菌株的生物多样性及生理特性进行了阐述;可培养盐碱细菌的数量及其多样性远远大于盐碱古菌,但是盐碱细菌对高盐度和强碱性p H依赖程度相对较低。盐碱细菌主要组成依次为芽孢杆菌纲(Bacilli,占总数约40%)、γ-变形菌纲(γ-Proteobacteria,30%)、梭菌纲(Clostridia,11%)、δ-变形菌纲(δ-Proteobacteria,6%)和放线菌纲(Actinobacteria,6%),而盐碱古菌主要组成为盐古菌纲(Halobacteria,92%)和甲烷微菌纲(Methanomicrobia,8%)。这些极端微生物在生物地球化学过程中或生态循环中扮演着重要的角色和功能,挖掘和利用盐碱菌具有重要意义。     

抗辐射菌Deinococcus radiodurans的多样性

抗辐射菌Deinococcus radiodurans是一种对电离辐射和其他DNA损伤因子具有极强抵抗能力的细菌,是研究DNA损伤与修复的模式生物。综述了国内外在抗辐射菌研究上取得的最新研究成果,从生存环境、对DNA损伤因子的抗性、抗性机理及其损伤修复关联基因等方面报道了抗辐射菌的多样性,并探讨了该细菌高效正确的DNA损伤修复机理的相关研究成果在生命科学、农业、环境修复及医学等领域的应用前景。     

中国温泉微生物物种多样性及其酶活性研究进展

微生物作为生物群体的重要组成成员,其生长受外界物化条件(如温度、盐度、pH等)影响较大。温泉作为极端水生环境之一,属于相对稳定且较为特殊的生态系统,使生长于其中的微生物可能具有适应高温等特殊生境的独特生存生理机制,具体表现为微生物物种及其活性次级代谢产物呈现出一定的多样性与新颖性。本文从菌株物种多样性分析及其酶活性研究方面,综述了近5年来国内温泉微生物相关研究进展,以期为温泉等极端环境微生物资源开发与保护提供参考。     

Microbial diversity and activity in Southern California salterns and bitterns: analogues for remnant ocean worlds

Concurrent osmotic and chaotropic stress make MgCl₂-rich brines extremely inhospitable environments. Understanding the limits of life in these brines is essential to the search for extraterrestrial life on contemporary and relict ocean worlds, like Mars, which could host similar environments. We sequenced environmental 16S rRNA genes and quantified microbial activity across a broad range of salinity and chaotropicity at a Mars-analogue salt harvesting facility in Southern California, where seawater is evaporated in a series of ponds ranging from kosmotropic NaCl brines to highly chaotropic MgCl₂ brines. Within NaCl brines, we observed a proliferation of specialized halophilic Euryarchaeota, which corresponded closely with the dominant taxa found in salterns around the world. These communities were characterized by very slow growth rates and high biomass accumulation. As salinity and chaotropicity increased, we found that the MgCl₂-rich brines eventually exceeded the limits of microbial activity. We found evidence that exogenous genetic material is preserved in these chaotropic brines, producing an unexpected increase in diversity in the presumably sterile MgCl₂-saturated brines. Because of their high potential for biomarker preservation, chaotropic brines could therefore serve as repositories of genetic biomarkers from nearby environments (both on Earth and beyond) making them prime targets for future life-detection missions.     

From genes to genomes: beyond biodiversity in Spain's Rio Tinto

Spain's Rio Tinto, or Red River, an example of an extremely acidic (pH 1.7-2.5) environment with a high metal content, teems with prokaryotic and eukaryotic microbial life. Our recent studies based on small-subunit rRNA genes reveal an unexpectedly high eukaryotic phylogenetic diversity in the river when compared to the relatively low prokaryotic diversity. Protists can therefore thrive in and dominate extremely acidic, heavy-metal-laden environments. Further, because we have discovered protistan acidophiles closely related to neutrophiles, we can hypothesize that the transition from neutral to acidic environments occurs rapidly over geological time scales. How have these organisms adapted to such environments? We are currently exploring the alterations in physiological mechanisms that might allow for growth of eukaryotic microbes at acid extremes. To this end, we are isolating phylogenetically diverse protists in order to characterize and compare ion-transporting ATPases from cultured acidophiles with those from neutrophilic counterparts. We predict that special properties of these ion transporters allow protists to survive in the Rio Tinto.     

Biodegradation of organic pollutants by halophilic bacteria and archaea

Hypersaline environments are important for both surface extension and ecological significance. As all other ecosystems, they are impacted by pollution. However, little information is available on the biodegradation of organic pollutants by halophilic microorganisms in such environments. In addition, it is estimated that 5% of industrial effluents are saline and hypersaline. Conventional nonextremophilic microorganisms are unable to efficiently perform the removal of organic pollutants at high salt concentrations. Halophilic microorganisms are metabolically different and are adapted to extreme salinity; these microorganisms are good candidates for the bioremediation of hypersaline environments and treatment of saline effluents. This literature survey indicates that both the moderately halophilic bacteria and the extremely halophilic archaea have a broader catabolic versatility and capability than previously thought. A diversity of contaminating compounds is susceptible to be degraded by halotolerant and halophile bacteria. Nevertheless, significant research efforts are still necessary in order to estimate the true potential of these microorganisms to be applied in environmental processes and in the remediation of contaminated hypersaline ecosystems. This effort should be also focused on basic research to understand the overall degradation mechanism, to identify the enzymes involved in the degradation process and the metabolism regulation.     

微生物高盐渗透适应策略及其耐盐强化研究进展

高盐废水因具有硬度高、可生化性差、水质成分复杂等特点,是较难处理的工业废水之一。现有物化处理技术存在运行成本高、处理效率低、二次污染重等诸多瓶颈。耐盐/嗜盐微生物可在高盐环境下进行正常生理代谢,因此,开发经济、高效、可靠的高盐废水生物处理技术有望成为高盐废水处理的主流方向之一。本文系统综述了耐盐/嗜盐微生物盐溶、胞内小分子相容溶质积累、蛋白质稳定和细胞表面稳定等高渗透压适应策略。由于嗜盐微生物存在生长条件苛刻、功能微生物种类稀缺等问题,因此,耐盐微生物在高盐废水处理的未来应用空间更大。最新研究发现强化调控技术(电、光、磁)可提升微生物的高渗透压适应能力,其中电调控技术或是未来高盐废水生物处理的重点研究方向。     

高盐环境可培养细菌噬菌体的研究进展

病毒广泛存在于各类环境中并担负着重要的生态功能,其中包括高盐环境。对高盐环境病毒的研究已成为极端环境微生物研究领域的新热点,目前已被报道的100多株盐病毒中,90多株感染古菌,仅有14株感染细菌。本文综述了目前已知的14株高盐环境细菌噬菌体的形态特征、盐度响应及基因组学的研究进展,并分析了高盐噬菌体的形态多样性、生存策略以及包含在基因组中的进化和起源信息,分析结果表明:高盐噬菌体以有尾噬菌体为主;它们具有广盐性(Euryhaline)的特征,盐度极大地影响其吸附和增殖;它们与非高盐环境噬菌体可能具有共同的起源。高盐噬菌体虽然历经近30年的研究历程,但仅有14株被分离与培养,所以其分离纯化是今后重要工作之一,且结合免培养技术揭示高盐噬菌体的多样性与生态功能是其研究的发展方向。     

Evolutionary divergence and salinity-mediated selection in halophilic archaea.

Halophilic (literally salt-loving) archaea are a highly evolved group of organisms that are uniquely able to survive in and exploit hypersaline environments. In this review, we examine the potential interplay between fluctuations in environmental salinity and the primary sequence and tertiary structure of halophilic proteins. The proteins of halophilic archaea are highly adapted and magnificently engineered to function in an intracellular milieu that is in ionic balance with an external environment containing between 2 and 5 M inorganic salt. To understand the nature of halophilic adaptation and to visualize this interplay, the sequences of genes encoding the L11, L1, L10, and L12 proteins of the large ribosome subunit and Mn/Fe superoxide dismutase proteins from three genera of halophilic archaea have been aligned and analyzed for the presence of synonymous and nonsynonymous nucleotide substitutions. Compared to homologous eubacterial genes, these halophilic genes exhibit an inordinately high proportion of nonsynonymous nucleotide substitutions that result in amino acid replacement in the encoded proteins. More than one-third of the replacements involve acidic amino acid residues. We suggest that fluctuations in environmental salinity provide the driving force for fixation of the excessive number of nonsynonymous substitutions. Tinkering with the number, location, and arrangement of acidic and other amino acid residues influences the fitness (i.e., hydrophobicity, surface hydration, and structural stability) of the halophilic protein. Tinkering is also evident at halophilic protein positions monomorphic or polymorphic for serine; more than one-third of these positions use both the TCN and the AGY serine codons, indicating that there have been multiple nonsynonymous substitutions at these positions. Our model suggests that fluctuating environmental salinity prevents optimization of fitness for many halophilic proteins and helps to explain the unusual evolutionary divergence of their encoding genes.     

The bioenergetic basis for the decrease in metabolic diversity at increasing salt concentrations: implications for the functioning of salt lake ecosystems

Examination of the microbial diversity in hypersaline lakes of increasing salt concentrations shows that certain types of dissimilatory metabolism do not occur at the highest salinities. Examples are methanogenesis from hydrogen and carbon dioxide or from acetate, dissimilatory sulfate reduction with oxidation of acetate, and autotrophic nitrification. The observations can be explained on the basis of the energetic cost of haloadaptation used by the different metabolic groups and the free-energy change associated with the dissimilatory reactions. All halophilic microorganisms spend large amounts of energy to maintain steep gradients of Na⁺ and K⁺concentrations across their cytoplasmic membrane. Most Bacteria and also the methanogenic Archaea produce high intracellular concentrations of organic osmotic solutes at a high energetic cost. The halophilic aerobic Archaea (order Halobacteriales) and the halophilic fermentative Bacteria (order Halanaerobiales) use KCl as the main intracellular solute. This strategy, while requiring far-reaching adaptations of the intracellular machinery, is energetically more favorable than production of organic compatible solutes. By combining information on the amount of energy available to each physiological group and the strategy used to cope with salt stress, a coherent model emerges that provides explanations for the upper salinity limit at which the different microbial conversions occur in hypersaline lakes.     

Modified coat protein forms the flexible spindle‐shaped virion of haloarchaeal virus His1

Extremophiles are found in all three domains of cellular life. However, hyperthermic and hypersaline environments are typically dominated by archaeal cells which also hold the records for the highest growth temperature and are able to grow even at saturated salinity. Hypersaline environments are rich of virus‐like particles, and spindle‐shaped virions resembling lemons are one of the most abundant virus morphotypes. Spindle‐shaped viruses are archaea‐specific as all the about 15 such virus isolates infect either hyperthermophilic or halophilic archaea. In the present work, we studied spindle‐shaped virus His1 infecting an extremely halophilic euryarchaeon, Haloarcula hispanica. We demonstrate that His1 tolerates a variety of salinities, even lower than that of seawater. The detailed analysis of the structural constituents showed that the His1 virion is composed of only one major and a few minor structural proteins. There is no lipid bilayer in the His1 virion but the major structural protein VP21 is most likely lipid modified. VP21 forms the virion capsid, and the lipid modification probably enables hydrophobic interactions leading to the flexible nature of the virion. Furthermore, we propose that euryarchaeal virus His1 may be related to crenarchaeal fuselloviruses, and that the short‐tailed spindle‐shaped viruses could form a structure‐based viral lineage.     

Growth Tolerance of Rhizobia Isolated from Sand Dune Legumes of the Southwest Coast of India

This paper describes the properties of rhizobia from extreme soil environments which are characterized by high temperatures, salt concentrations and also rather extreme pH values due to the contamination by spray water from the sea. Coastal sand dunes are such extreme habitats which support a variety of microorganisms. To explore stress‐tolerant rhizobia, ten rhizobial strains were isolated from five wild legumes from two dune systems of the southwest coast of India. They were tested for growth performance or tolerance at a wide range of temperatures (30–55 °C), salinity (0.1–4.5 % w/v) and initial pH values (3.5–11). Growth of five isolates was highest between 30–40 °C, while four isolates showed considerable growth up to 2.5 % salinity (at 35 °C). All isolates demonstrated elevated growth at an initial pH of between 5–6 (at 35 °C and 2 % salinity), while five isolates had additional growth peaks at an initial pH of between pH 7.5–9 indicating alkaline tolerance and were suitable for efficient phosphate solubilization. The stress tolerance traits of these rhizobia are of potential value for strain improvement in agriculture or the bioremediation of soils at elevated temperatures, salinity and extreme pH values, and thus are of high biotechnological importance.     

Porphyromonas gingivalis: an invasive and evasive opportunistic oral pathogen

Archaea that live at high salt concentrations are a phylogenetically diverse group of microorganisms. They include the heterotrophic haloarchaea (class Halobacteria) and some methanogenic Archaea, and they inhabit both oxic and anoxic environments. In spite of their common hypersaline environment, halophilic archaea are surprisingly diverse in their nutritional demands, range of carbon sources degraded (including hydrocarbons and aromatic compounds) and metabolic pathways. The recent discovery of a new group of extremely halophilic Euryarchaeota, the yet uncultured Nanohaloarchaea, shows that the archaeal diversity and metabolic variability in hypersaline environments is higher than hitherto estimated.     

Catabolic versatility of aromatic compound-degrading halophilic bacteria

There is growing interest in the development and optimization of bioremediation processes to deal with environments with high salinity that are contaminated with aromatic compounds. To estimate the diversity of moderately halophilic bacteria that could be used in such processes, enrichments were performed based on growth with a variety of aromatic compounds including phenol as a model pollutant. A group of bacteria that were able to grow over a wide range of salt concentrations were isolated, with the majority of these assigned to the genus Halomonas using phenotypic features and 16S rRNA sequences comparison. PCR amplification with degenerate primers revealed the presence in these isolates of genes encoding ring-cleaving enzymes in the beta-ketoadipate pathway for aromatic catabolism: catechol 1,2-dioxygenase and protocatechuate 3,4-dioxygenase. Furthermore, the activity of these two enzymes was detected in the newly described species Halomonas organivorans. Together, these studies indicate that moderately halophilic bacteria have the potential to catabolize aromatic compounds in environments with high salinity.     

Evolution of bacterial flora from a subterranean saline well by graduated salinity changes in enrichment media

The bacterial flora of samples taken from a subterranean saline well was enriched (1) by periodic salinity increase and (2) by periodic salinity decrease, both at 25° and 35°C. During the enrichment process, bacterial flora, including halotolerant, marine, moderately and extremely halophilic bacteria, were enumerated. Results were similar at both temperatures. Marine bacteria and moderately halophilic microorganisms were the most favoured groups, predominating between 3 and 30% (w/v) salt content; extremely halophilic bacteria also appeared when salinity reached 30% (w/v) and halotolerant bacteria were poorly represented. The taxonomic distribution of 125 selected strains, chosen at random from counting media, was essentially similar to those from other hypersaline environments.     

Bioenergetic aspects of halophilism.

Examination of microbial diversity in environments of increasing salt concentrations indicates that certain types of dissimilatory metabolism do not occur at the highest salinities. Examples are methanogenesis for H2 + CO2 or from acetate, dissimilatory sulfate reduction with oxidation of acetate, and autotrophic nitrification. Occurrence of the different metabolic types is correlated with the free-energy change associated with the dissimilatory reactions. Life at high salt concentrations is energetically expensive. Most bacteria and also the methanogenic Archaea produce high intracellular concentrations of organic osmotic solutes at a high energetic cost. All halophilic microorganisms expend large amounts of energy to maintain steep gradients of NA+ and K+ concentrations across their cytoplasmic membrane. The energetic cost of salt adaptation probably dictates what types of metabolism can support life at the highest salt concentrations. Use of KCl as an intracellular solute, while requiring far-reaching adaptations of the intracellular machinery, is energetically more favorable than production of organic-compatible solutes. This may explain why the anaerobic halophilic fermentative bacteria (order Haloanaerobiales) use this strategy and also why halophilic homoacetogenic bacteria that produce acetate from H2 + CO2 exist whereas methanogens that use the same substrates in a reaction with a similar free-energy yield do not.     

Genome sequence of Oceanobacillus iheyensis isolated from the Iheya Ridge and its unexpected adaptive capabilities to extreme environments

Oceanobacillus iheyensis HTE831 is an alkaliphilic and extremely halotolerant Bacillus-related species isolated from deep-sea sediment. We present here the complete genome sequence of HTE831 along with analyses of genes required for adaptation to highly alkaline and saline environments. The genome consists of 3.6 Mb, encoding many proteins potentially associated with roles in regulation of intracellular osmotic pressure and pH homeostasis. The candidate genes involved in alkaliphily were determined based on comparative analysis with three Bacillus species and two other Gram-positive species. Comparison with the genomes of other major Gram-positive bacterial species suggests that the backbone of the genus Bacillus is composed of approximately 350 genes. This second genome sequence of an alkaliphilic Bacillus-related species will be useful in understanding life in highly alkaline environments and microbial diversity within the ubiquitous bacilli.     

Extracellular Ca2(+)-dependent inducible alkaline phosphatase from extremely halophilic archaebacterium Haloarcula marismortui.

When starved of inorganic phosphate, the extremely halophilic archaebacterium Haloarcula marismortui produces the enzyme alkaline phosphatase and secretes it to the medium. This inducible extracellular enzyme is a glycoprotein whose subunit molecular mass is 160 kDa, as estimated by sodium dodecyl sulfate-gel electrophoresis. The native form of the enzyme is heterogeneous and composed of multiple oligomeric forms. The enzymatic activity of the halophilic alkaline phosphatase is maximal at pH 8.5, and the enzyme is inhibited by phosphate. Unlike most alkaline phosphatases, the halobacterial enzyme requires Ca2+ and not Zn2+ ions for its activity. Both calcium ions (in the millimolar range) and NaCl (in the molar range) are required for the stability of the enzyme.