嗜盐放线菌资源及次生代谢产物研究进展

嗜盐放线菌是重要的极端微生物资源,因其独特的生长环境、生理机制而备受关注。本文对嗜盐放线菌的定义、生物多样性及次生代谢产物的研究进展进行综述。结合我国嗜盐放线菌的研究现状,分析尚存在的问题及其发展前景。     

宏基因组技术在开发极端环境未培养微生物中的应用

人类对自然环境中约99％的微生物不能用传统的方法进行纯培养,对于极端环境中的微生物更是知之甚少.随着宏基因组技术的出现,人们可对选一庞大的未知世界进行多方面研究.目前研究者利用这一技术已经对地球上的多种极端生境进行了研究,并取得了很多新的成就.简要概述这一技术在极端环境未培养微生物研究中的应用.     

Life in blue: Copper resistance mechanisms of bacteria and Archaea used in industrial biomining of minerals

Industrial biomining processes to extract copper, gold and other metals involve the use of extremophiles such as the acidophilic Acidithiobacillus ferrooxidans (Bacteria), and the thermoacidophilic Sulfolobus metallicus (Archaea). Together with other extremophiles these microorganisms subsist in habitats where they are exposed to copper concentrations higher than 100 mM. Herein we review the current knowledge on the Cu-resistance mechanisms found in these microorganisms. Recent information suggests that biomining extremophiles respond to extremely high Cu concentrations by using simultaneously all or most of the following key elements: 1) a wide repertoire of Cu-resistance determinants; 2) duplication of some of these Cu-resistance determinants; 3) existence of novel Cu chaperones; 4) a polyP-based Cu-resistance system, and 5) an oxidative stress defense system. Further insight of the biomining community members and their individual response to copper is highly relevant, since this could provide key information to the mining industry. In turn, this information could be used to select the more fit members of the bioleaching community to attain more efficient industrial biomining processes.     

Can zoosporic true fungi grow or survive in extreme or stressful environments?

Zoosporic true fungi are thought to be ubiquitous in many ecosystems, especially in cool, moist soils and freshwater habitats which are rich in organic matter. However, some of the habitats where these fungi are found may periodically experience extreme conditions, such as soils in extremely dry, hot and cold climates, acidic and alkaline soils, polluted rivers, anaerobic soil and water, saline soil and water, periglacial soils, oligotrophic soils, tree canopies and hydrothermal vents. It is clear that many ecotypes of zoosporic true fungi have indeed adapted to extreme or stressful environmental conditions. This conclusion is supported by studies in both the field and in the laboratory. Therefore, in our opinion, at least some true zoosporic fungi can be considered to be extremophiles.     

Enrichment culture and microscopy conceal diverse thermophilic Synechococcus populations in a single hot spring microbial mat habitat

Recent molecular studies have shown a great disparity between naturally occurring and cultivated microorganisms. We investigated the basis for disparity by studying thermophilic unicellular cyanobacteria whose morphologic simplicity suggested that a single cosmopolitan species exists in hot spring microbial mats worldwide. We found that partial 16S rRNA sequences for all thermophilic Synechococcus culture collection strains from diverse habitats are identical. Through oligonucleotide probe analysis and cultivation, we provide evidence that this species is strongly selected for in laboratory culture to the exclusion of many more-predominant cyanobacterial species coexisting in the Octopus Spring mat in Yellowstone National Park. The phylogenetic diversity among Octopus Spring cyanobacteria is of similar magnitude to that exhibited by all cyanobacteria so far investigated. We obtained axenic isolates of two predominant cyanobacterial species by diluting inocula prior to enrichment. One isolate has a 16S rRNA sequence we have not yet detected by cloning. The other has a 16S rRNA sequence identical to a new cloned sequence we report herein. This is the first cultivated species whose 16S rRNA sequence has been detected in this mat system by cloning. We infer that biodiversity within this community is linked to guild structure.     

Enrichment culture and microscopy conceal diverse thermophilic Synechococcus populations in a single hot spring microbial mat habitat.

Recent molecular studies have shown a great disparity between naturally occurring and cultivated microorganisms. We investigated the basis for disparity by studying thermophilic unicellular cyanobacteria whose morphologic simplicity suggested that a single cosmopolitan species exists in hot spring microbial mats worldwide. We found that partial 16S rRNA sequences for all thermophilic Synechococcus culture collection strains from diverse habitats are identical. Through oligonucleotide probe analysis and cultivation, we provide evidence that this species is strongly selected for in laboratory culture to the exclusion of many more-predominant cyanobacterial species coexisting in the Octopus Spring mat in Yellowstone National Park. The phylogenetic diversity among Octopus Spring cyanobacteria is of similar magnitude to that exhibited by all cyanobacteria so far investigated. We obtained axenic isolates of two predominant cyanobacterial species by diluting inocula prior to enrichment. One isolate has a 16S rRNA sequence we have not yet detected by cloning. The other has a 16S rRNA sequence identical to a new cloned sequence we report herein. This is the first cultivated species whose 16S rRNA sequence has been detected in this mat system by cloning. We infer that biodiversity within this community is linked to guild structure.     

Combining virtual and in-place field crews to model pollinator species shift in the Greater Yellowstone Ecosystem

Insect pollinators (bees and butterflies) face global challenges as climate change impacts species occurrence (or extinction) within managed and protected areas. While species decline is predicted for invertebrate species, especially in sensitive ecosystems such as high alpine systems, little is known about species responses to climate change. This study seeks to understand the impact of climate change on pollinators in high elevation ecosystems, specifically within Yellowstone and Grand Teton National Parks. These parks are connected protected areas in the United States that act as a large reservoir for conserving species, including pollinators. Students performing research amidst the COVID-19 pandemic were divided into two virtual teams (bug team and climate team) to assess historic climate data, natural history collections and plant/pollinator data from Yellowstone and Grand Teton National Parks. Each team was tasked with addressing the larger question of climate change impacts on pollinators within protected areas while also gaining interpersonal, collaborative learning skills through their experience. This paper highlights two case studies tied to pollinator decline. The first assesses citizen science and natural history collection databases to predict and field test species occurrence within the parks. The second identifies suitable habitats for species occurrence locations. Lastly, this paper emphasizes the learning outcomes students had from virtual and hybrid field settings and offers suggestions for applications towards field-based research efforts.     

Environmental Pressure May Change the Composition Protein Disorder in Prokaryotes

Many prokaryotic organisms have adapted to incredibly extreme habitats. The genomes of such extremophiles differ from their non-extremophile relatives. For example, some proteins in thermophiles sustain high temperatures by being more compact than homologs in non-extremophiles. Conversely, some proteins have increased volumes to compensate for freezing effects in psychrophiles that survive in the cold. Here, we revealed that some differences in organisms surviving in extreme habitats correlate with a simple single feature, namely the fraction of proteins predicted to have long disordered regions. We predicted disorder with different methods for 46 completely sequenced organisms from diverse habitats and found a correlation between protein disorder and the extremity of the environment. More specifically, the overall percentage of proteins with long disordered regions tended to be more similar between organisms of similar habitats than between organisms of similar taxonomy. For example, predictions tended to detect substantially more proteins with long disordered regions in prokaryotic halophiles (survive high salt) than in their taxonomic neighbors. Another peculiar environment is that of high radiation survived, e.g. by Deinococcus radiodurans. The relatively high fraction of disorder predicted in this extremophile might provide a shield against mutations. Although our analysis fails to establish causation, the observed correlation between such a simplistic, coarse-grained, microscopic molecular feature (disorder content) and a macroscopic variable (habitat) remains stunning.     

Lithobiontic life: “Atacama rocks are well and alive”

Our knowledge on the Microbiology of the Atacama Desert has increased steadily and substantially during the last two decades. This information now supports a paradigmatic change on the Atacama Desert from a sterile, uninhabitable territory to a hyperarid region colonized by a rich microbiota that includes extremophiles and extreme-tolerant microorganisms. Also, extensive reports are available on the prevalent physical and chemical environmental conditions, ecological niches and, the abundance, diversity and organization of the microbial life in the Atacama Desert. This territory is a highly desiccated environment due to the absence of regular rain events. Liquid water scarcity is the most serious environmental factor affecting the Atacama Desert microorganisms. The intense solar irradiation in this region contributes, in a synergistic fashion with desiccation, to limit the survival and growth of the microbial life. In order to overcome these two extreme conditions, successful microorganisms, organized as microbial consortia, take advantage of (a) the physical characteristics of lithic habitats, which provide sites for colonization on, within or below the rock substrate, the attenuation and filtration of the intense solar irradiation and, the collection of liquid water from incoming fog formations and by water vapour condensation and deliquescence on or within their surfaces, and (b) the biological adaptations of members of the microbial communities that allow them to synthesize hydrophilic macromolecules, antioxidants and UV-light absorbents. Lithic habitats have been considered specialized shelters where life forms can reach protection at environments subjected to extremes of desiccation and solar irradiation, here on Earth or elsewhere. This review is an overview of part of the scientific information collected on lithobionts from the Atacama Desert, their rock substrates and their strategies to cope with extremes of desiccation and intense photosynthetic active radiation and UV irradiations.     

深海极端微生物菌群及代谢产物多样性的研究进展

海洋覆盖了地球表面积的四分之三,它不仅是生命的起源,而且还孕育了各种极端微生物。它们存在于海洋极端环境中,如热液喷口、热泉、咸湖和深海层等,由于生境太过恶劣,一度被认为是生命的禁区。随着人类对深海极端环境微生物研究的不断深入,已经探索到那里具有丰富的菌群资源和具有潜在价值的天然生物活性产物。这些极端微生物能够适应极高温、极低温、高压、高盐、高放射性和极度酸碱性等极端环境,具有特殊的生物多样性、遗传背景和代谢途径,能够产生各种具有特殊功能的酶类及其他活性物质,展现出巨大的研究价值和应用潜力。研究海洋极端微生物对探索生物多样性、新资源开发利用及对地球生物学研究等都具有重要意义。     

PCR detection and analysis of the free-living amoeba Naegleria in hot springs in Yellowstone and Grand Teton National Parks

Free-living thermotolerant amoebae pose a significant health risk to people who soak and swim in habitats suitable for their growth, such as hot springs. In this survey of 23 different hot springs in Yellowstone and Grand Teton National Parks, we used PCR with primer sets specific for Naegleria to detect three sequence types that represent species not previously described, as well as a fourth sequence type identified as the pathogen Naegleria fowleri.     

Extremophiles: radiation resistance microbial reserves and therapeutic implications

Micro‐organisms with the ability to survive in extreme environmental conditions are known as ‘extremophiles’. Currently, extremophiles have caused a sensation in the biotechnology/pharmaceutical industries with their novel compounds, known as ‘extremolytes’. The potential applications of extremolytes are being investigated for human therapeutics including anticancer drugs, antioxidants, cell cycle‐blocking agents, anticholesteric drugs, etc. It is hypothesized that the majority of ultraviolet radiation (UVR)‐resistant micro‐organisms can be used to develop anticancer drugs to prevent skin damage from UVR. The metabolites from UVR‐resistant microbes are a great source of potential therapeutic applications in humans. This article aims to discuss the potentials of extremolytes along with their therapeutic implications of UVR extremophiles. The major challenges of therapeutic development using extremophiles are also discussed.     

Effects of extreme habitat conditions on otolith morphology: a case study on extremophile live bearing fishes (Poecilia mexicana, P. sulphuraria)

Our study was designed to evaluate if, and to what extent, restrictive environmental conditions affect otolith morphology. As a model, we chose two extremophile livebearing fishes: (i) Poecilia mexicana, a widespread species in various Mexican freshwater habitats, with locally adapted populations thriving in habitats characterized by the presence of one (or both) of the natural stressors hydrogen sulphide and darkness, and (ii) the closely related Poecilia sulphuraria living in a highly sulphidic habitat (Baños del Azufre). All three otolith types (lapilli, sagittae, and asterisci) of P. mexicana showed a decrease in size ranging from the non-sulphidic cave habitat (Cueva Luna Azufre), to non-sulphidic surface habitats, to the sulphidic cave (Cueva del Azufre), to sulphidic surface habitats (El Azufre), to P. sulphuraria. Although we found a distinct differentiation between ecotypes with respect to their otolith morphology, no clear-cut pattern of trait evolution along the two ecological gradients was discernible. Otoliths from extremophiles captured in the wild revealed only slight similarities to aberrant otoliths found in captive-bred fish. We therefore hypothesize that extremophile fishes have developed coping mechanisms enabling them to avoid aberrant otolith growth – an otherwise common phenomenon in fishes reared under stressful conditions.     

Ciliates in Extreme Environments

As eukaryotic microbial life, ciliated protozoan may be found actively growing in some extreme condition where there is a sufficient energy source to sustain it because they are exceedingly adaptable and not notably less adaptable than the prokaryotes. However, a crucial problem in the study of ciliates in extreme environments is the lack of reliable cultivation techniques. To our knowledge, only a tiny fraction of ciliates can be cultured in the laboratory, even for a very limited period, which can partly explain the paucity of our understanding about ciliates diversity in various extremes although the interest in the biodiversity of extremophiles increased significantly during the past three decades. This mini‐review aims to compile the knowledge of several groups of free‐living ciliates that can be microscopically observed in extreme environmental samples, although most habitats have not been sufficiently well explored for sound generalizations.     

New opportunities revealed by biotechnological explorations of extremophiles

Over the past few decades the extremes at which life thrives has continued to challenge our understanding of biochemistry, biology and evolution. As more new extremophiles are brought into laboratory culture, they have provided a multitude of potential applications for biotechnology. More recently, innovative culturing approaches, environmental genome sequencing and whole genome sequencing have provided new opportunities for the biotechnological exploration of extremophiles.     

PCR Detection and Analysis of the Free-Living Amoeba Naegleria in Hot Springs in Yellowstone and Grand Teton National Parks

Free-living thermotolerant amoebae pose a significant health risk to people who soak and swim in habitats suitable for their growth, such as hot springs. In this survey of 23 different hot springs in Yellowstone and Grand Teton National Parks, we used PCR with primer sets specific for Naegleria to detect three sequence types that represent species not previously described, as well as a fourth sequence type identified as the pathogen Naegleria fowleri.     

Migrations and swimming capabilities of endangered pallid sturgeon (Scaphirhynchus albus) to guide passage designs in the fragmented Yellowstone River

Fragmentation of the Yellowstone River is hypothesized to preclude recruitment of endangered Scaphirhynchus albus (pallid sturgeon) by impeding upstream spawning migrations and access to upstream spawning areas, thereby limiting the length of free‐flowing river required for survival of early life stages. Building on this hypothesis, the reach of the Yellowstone River affected by Intake Diversion Dam (IDD) is targeted for modification. Structures including a rock ramp and by‐pass channel have been proposed as restoration alternatives to facilitate passage. Limited information on migrations and swimming capabilities of pallid sturgeon is available to guide engineering design specifications for the proposed structures. Migration behavior, pathways (channel routes used during migrations), and swimming capabilities of free‐ranging wild adult pallid sturgeon were examined using radiotelemetry, and complemented with hydraulic data obtained along the migration pathways. Migrations of 12–26% of the telemetered pallid sturgeon population persisted to IDD, but upstream passage over the dam was not detected. Observed migration pathways occurred primarily through main channel habitats; however, migrations through side channels up to 3.9 km in length were documented. The majority of pallid sturgeon used depths of 2.2–3.4 m and mean water velocities of 0.89–1.83 m/s while migrating. Results provide inferences on depths, velocities, and habitat heterogeneity of reaches successfully negotiated by pallid sturgeon that may be used to guide designs for structures facilitating passage at IDD. Passage will provide connectivity to potential upstream spawning areas on the Yellowstone River, thereby increasing the likelihood of recruitment for this endangered species.     

Extremotolerance in fungi: evolution on the edge

Our planet offers many opportunities for life on the edge: high and low temperatures, high salt concentrations, acidic and basic conditions and toxic environments, to name but a few extremes. Recent studies have revealed the diversity of fungi that can occur in stressful environments that are hostile to most eukaryotes. We review these studies here, with the additional purpose of proposing some mechanisms that would allow for the evolutionary adaptation of eukaryotic microbial life under extreme conditions. We focus, in particular, on life in ice and life at high salt concentrations, as there is a surprising similarity between the fungal populations in these two kinds of environments, both of which are characterized by low water activity. We propose steps of evolution of generalist species towards the development of specialists in extreme habitats. We argue that traits present in some fungal groups, such as asexuality, synthesis of melanin-like pigments and a flexible morphology, are preadaptations that facilitate persistence and eventual adaptation to conditions on the ecological edge, as well as biotope switches. These processes are important for understanding the evolution of extremophiles; moreover, they have implications for the emergence of novel fungal pathogens.     

129 Cryptoendolithic Photosynthetic Communities Within Recent and Ancient Travertine in Yellowstone National Park

Travertine terraces have been deposited by calcareous hot springs in Yellowstone from as early as 365,000 years to the present. Most of these porous and non‐porous CaCO3 rocks (old or new) contain a 1–2 mm thick greenish band about 1–3 mm below the upper surface. These bands are composed of cyanobacteria and, sometimes, unicellular green algae. Although some moisture may be retained for much of the year, all undergo freezing in winter and desiccation in summer. DGGE (denaturing gradient gel electrophoresis), with subsequent 16S rDNA sequence analyses of bands, has shown that relatively few phylotypes of cyanobacteria are present, but some occur in travertine of very different ages, indicating secondary establishment of the communities. Clonal cultures of predominant types have also been established and sequenced. All those tested are able to survive extreme desiccation. Preliminary sequence analyses of cultures show that some strains are nearly identical to known cyanobacterial strains while others show little similarity. One sequence is 100% identical to the cyanobacterium Cyanobium gracile. This cyanobacterium is known to be distributed worldwide in lakes and brackish seas, but not in a cryptoendolithic environment. Another sequence shows 99% identity to two cyanobacteria isolated from Antarctic freshwater ponds. Both Antarctic ponds and Yellowstone travertine are environments in which adaptations for desiccation and/or freezing tolerance could be crucial. The lack of ecological similarity among some of these strains indicates that genes other than 16S rDNA must be used for differentiation. These results will be discussed along with the ecology of travertine habitats.