Molecular microbial diversity of a spacecraft assembly facility

In ongoing investigations to map and archive the microbial footprints in various components of the spacecraft and its accessories, we have examined the microbial populations of the Jet Propulsion Laboratory's Spacecraft Assembly Facility (JPL-SAF). Witness plates made up of spacecraft materials, some painted with spacecraft qualified paints, were exposed for 7 to 9 months at JPL-SAF and examined the particulate materials collected for the incidence of total cultivable aerobic heterotrophs and heat-tolerant (80°C for 15-min.) spore-formers. The results showed that the witness plates coated with spacecraft qualified paints attracted more dust particles than the non-coated stainless steel witness plates. Among the four paints tested, witness plates coated with NS43G accumulated the highest number of particles, and hence attracted more cultivable microbes. The conventional microbiological examination revealed that the JPL-SAF harbors mainly Gram-positive microbes and mostly spore-forming Bacillus species. Most of the isolated microbes were heat resistant to 80°C and proliferate at 60°C. The phylogenetic relationships among 23 cultivable heat-tolerant microbes were examined using a battery of morphological, physiological, molecular and chemotaxonomic characterizations. By 16S rDNA sequence analysis, the isolates fell into seven clades:Bacillus licheniformis, B. pumilus, B. cereus, B. circulans, Staphylococcus capitis, Planococcus sp. and Micrococcus lylae. In contrast to the cultivable approach, direct DNA isolation, cloning and 16S rDNA sequencing analysis revealed equal representation of both Gram-positive and Gram-negative microorganisms.     

Microbial Monitoring of Spacecraft and Associated Environments

Rapid microbial monitoring technologies are invaluable in assessing contamination of spacecraft and associated environments. Universal and widespread elements of microbial structure and chemistry are logical targets for assessing microbial burden. Several biomarkers such as ATP, LPS, and DNA (ribosomal or spore-specific), were targeted to quantify either total bioburden or specific types of microbial contamination. The findings of these assays were compared with conventional, culture-dependent methods. This review evaluates the applicability and efficacy of some of these methods in monitoring the microbial burden of spacecraft and associated environments. Samples were collected from the surfaces of spacecraft, from surfaces of assembly facilities, and from drinking water reservoirs aboard the International Space Station (ISS). Culture-dependent techniques found species of Bacillus to be dominant on these surfaces. In contrast, rapid, culture-independent techniques revealed the presence of many Gram-positive and Gram-negative microorganisms, as well as actinomycetes and fungi. These included both cultivable and noncultivable microbes, findings further confirmed by DNA-based microbial detection techniques. Although the ISS drinking water was devoid of cultivable microbes, molecular-based techniques retrieved DNA sequences of numerous opportunistic pathogens. Each of the methods tested in this study has its advantages, and by coupling two or more of these techniques even more reliable information as to microbial burden is rapidly obtained.     

Pyrosequencing-derived bacterial, archaeal, and fungal diversity of spacecraft hardware destined for Mars

Spacecraft hardware and assembly cleanroom surfaces (233 m(2) in total) were sampled, total genomic DNA was extracted, hypervariable regions of the 16S rRNA gene (bacteria and archaea) and ribosomal internal transcribed spacer (ITS) region (fungi) were subjected to 454 tag-encoded pyrosequencing PCR amplification, and 203,852 resulting high-quality sequences were analyzed. Bioinformatic analyses revealed correlations between operational taxonomic unit (OTU) abundance and certain sample characteristics, such as source (cleanroom floor, ground support equipment [GSE], or spacecraft hardware), cleaning regimen applied, and location about the facility or spacecraft. National Aeronautics and Space Administration (NASA) cleanroom floor and GSE surfaces gave rise to a larger number of diverse bacterial communities (619 OTU; 20 m(2)) than colocated spacecraft hardware (187 OTU; 162 m(2)). In contrast to the results of bacterial pyrosequencing, where at least some sequences were generated from each of the 31 sample sets examined, only 13 and 18 of these sample sets gave rise to archaeal and fungal sequences, respectively. As was the case for bacteria, the abundance of fungal OTU in the GSE surface samples dramatically diminished (9× less) once cleaning protocols had been applied. The presence of OTU representative of actinobacteria, deinococci, acidobacteria, firmicutes, and proteobacteria on spacecraft surfaces suggests that certain bacterial lineages persist even following rigorous quality control and cleaning practices. The majority of bacterial OTU observed as being recurrent belonged to actinobacteria and alphaproteobacteria, supporting the hypothesis that the measures of cleanliness exerted in spacecraft assembly cleanrooms (SAC) inadvertently select for the organisms which are the most fit to survive long journeys in space.     

Development of a simple cultivation method for isolating hitherto-uncultured cellulase-producing microbes

Although enrichment culture is typically employed to isolate cellulolytic microbes, this approach tends to favor fast-growing species and discriminates against all others. Therefore, efforts to prevent the overgrowth of fast-growing species are necessary to isolate novel cellulase-producing strains. In this study, we developed a simple culture method for isolating hitherto-uncultured microbes that possess cellulase activity, particularly exocellulase. In this method, the microbial source (a forest soil) was suspended in sterilized water and inoculated onto a mineral salts agar medium, which was then overlaid with filter paper to sandwich the microbial suspension between the agar surface and paper. The filter paper fibers served to immobilize the microbial cells and were the dominant carbon source. Following cultivation at 30°C for 2 weeks, emerging colonies were isolated based on their morphology and were then subjected to phylogenetic and enzyme analyses. Using this method, 2,150 CFUs/g dry soil were obtained, and the ratio of fungal to bacterial isolates was approximately 4:1. Phylogenetic analyses revealed that most fungal and bacterial isolates belong to ten and two genera, respectively. Notably, all isolates possessed exocellulase activity, and several strains showed strong activity that was comparable to Trichoderma cellulase. Many isolates also exhibited cellulase and xylanase activity, and several strains possessed laccase activity. It is expected that the culture method described here will be useful for the isolation of hitherto-uncultured cellulolytic microbes and the identification of novel cellulases.     

Screening of microbes,isolation, genetic manipulation,and physiological optimization of Brevibacterium helvolum to produce and excrete thymidine and deoxyuridine in high concentrations

Analogues of deoxypyrimidines are used in the treatment of a variety of human ailments. Azidothymidine, or AZT, is one such analogue used to treat AIDS. Thymidine is the precursor of AZT, and its cost contributes to the high price of AZT. Attempts are being made to isolate and genetically manipulate microbes that can produce and excrete this compound in high concentrations. To this end, 145 different microbial species from Zeneca and the American Type Culture Collection were screened. Moreover, soil samples were collected from 36 different sites in England, and microbes from these samples were isolated and screened. >From approximately 25,000 isolates screened as single colonies and from 4,000 in liquid cultures, a strain of Brevibacterium helvolum showed the most promising results. Pyrimidine metabolic pathways of this bacterium were worked out, the isolate was genetically manipulated, and physiological conditions were optimized to increase the production of thymidine and deoxyuridine. These mutants of B. helvolum are considered to be of commercial importance.     

瘤胃木质纤维素降解菌及降解酶基因的研究进展

反刍动物瘤胃是公认的木质纤维素高效降解的天然反应器,对瘤胃微生物的研究已成为开发生物能源的热点领域之一。目前的研究手段已经从传统的依赖分离培养从瘤胃中获得木质纤维素降解菌,并对降解菌中的木质纤维素降解酶逐一分析,发展到通过基因组/元基因组学技术,直接从瘤胃中发现并获得大量新的木质纤维素降解酶基因/基因簇,进而探讨其降解的分子机理。已有的研究结果表明,瘤胃微生物降解木质纤维素的过程非常复杂,涉及大量不同种类的微生物及基因/基因簇,随着新分析技术的建立和完善,对这些微生物和基因的研究已取得了诸多进展。本论文综述了近期有关该方向的研究进展。     

毛细管电泳在微生物分离与检测中的应用

毛细管电泳在分离与分析无机离子、有机小分子、生物大分子(如蛋白质、核酸)和微生物(细菌、病毒)等方面应用十分广泛。着重论述了毛细管电泳在微生物分离与检测方面的基本原理、早期探索、存在问题和最新进展。     

武汉亮斑扁角水虻幼虫肠道微生物对其成虫产卵行为的影响

研究武汉亮斑扁角水虻幼虫肠道微生物对武汉亮斑水虻成虫产卵行为的影响。首先使用LB(Luria-Bertani)培养基对武汉亮斑水虻幼虫肠道微生物进行分离纯培养,筛选得到23株肠道微生物。以灭菌的LB液体培养基为阴性对照,使用已证实引诱产卵效果好的来自武汉亮斑水虻卵表的属于戈登氏菌属的细菌(Gordonia sihwensis)FE06为阳性对照,利用筛选到的武汉亮斑水虻幼虫肠道微生物摇瓶发酵液对武汉亮斑水虻成虫进行产卵行为实验。发现有5株武汉亮斑水虻幼虫肠道微生物(BSFLG01、BSFLG03、BSFLG04、BSFLG05、BSFLG06)对武汉亮斑水虻产卵有显著的积极促进作用,其中3株(BSFLG03、BSFLG05、BSFLG06)对水虻成虫产卵的引诱作用明显强于所设立的阳性对照FE06;菌株BSFLG07为一种毕赤酵母菌(Pichia kudriavzevii),对武汉亮斑水虻产卵有消极影响。经菌落培养特征、菌体形态比较、16SrDNA或18SrDNA序列测定和发育树比对分析,鉴定出这5种具有显著引诱武汉亮斑水虻产卵作用的微生物分别为:枯草芽胞杆菌(Bacillus subtilis)BSFLG01、一种沙雷氏菌(Serratiasp.)BSFLG03、库德毕赤酵母(Pichia kudriavzevii)BSFLG04、皱落假丝酵母(Candida rugosas)BSFLG05、粘质沙雷氏菌(Serratia marcescens)BSFLG06。     

Autoradiographic method to screen for soil microorganisms which accumulate zinc.

An autoradiographic method was developed to screen for and isolate soil microorganisms which accumulate zinc (Zn). Diluted soil samples (Rubicon fine sand, Entic Haplorthods [pH 5.9]) were plated on soil extract-glucose agar containing radioactive 65Zn. After 7 days of incubation, individual colonies which accumulated sufficient 65Zn could be detected by autoradiography. These colonies were isolated and confirmed as Zn accumulators in pure culture by using the autoradiographic plate technique. Most Zn accumulators were filamentous fungi, identified as Penicillium janthinellum, Aspergillus fumigatus, and Paecilomyces sp. Isolates of Penicillium janthinellum were the most common Zn accumulators. The most abundant Zn-accumulating bacteria were Bacillus spp. The validity of the autoradiographic plate technique to differentiate soil microbes which accumulate Zn was examined independently by energy dispersive X-ray analysis in a scanning electron microscope. This method confirmed that fungal isolates which gave positive autoradiographic responses in the plate assay bioaccumulated more Zn in their biomass than fungal isolates from the same soil sample which gave negative autoradiographic responses. Thus, this technique can be applied to specifically screen for and isolate microbes from the environment which bioaccumulate Zn.     

Autoradiographic method to screen for soil microorganisms which accumulate zinc

An autoradiographic method was developed to screen for and isolate soil microorganisms which accumulate zinc (Zn). Diluted soil samples (Rubicon fine sand, Entic Haplorthods [pH 5.9]) were plated on soil extract-glucose agar containing radioactive 65Zn. After 7 days of incubation, individual colonies which accumulated sufficient 65Zn could be detected by autoradiography. These colonies were isolated and confirmed as Zn accumulators in pure culture by using the autoradiographic plate technique. Most Zn accumulators were filamentous fungi, identified as Penicillium janthinellum, Aspergillus fumigatus, and Paecilomyces sp. Isolates of Penicillium janthinellum were the most common Zn accumulators. The most abundant Zn-accumulating bacteria were Bacillus spp. The validity of the autoradiographic plate technique to differentiate soil microbes which accumulate Zn was examined independently by energy dispersive X-ray analysis in a scanning electron microscope. This method confirmed that fungal isolates which gave positive autoradiographic responses in the plate assay bioaccumulated more Zn in their biomass than fungal isolates from the same soil sample which gave negative autoradiographic responses. Thus, this technique can be applied to specifically screen for and isolate microbes from the environment which bioaccumulate Zn.     

Thermophiles: A life at elevated temperatures

Interest in the ecology, physiology and evolution of microorganisms adapted to growth at relatively high temperatures (up to 110°C) has increased enormously during the past two decades. This interest was stimulated by the discovery of marine hydrothermal vent ecosystems, and also by awareness of the potential of thermophilic microbes in biotechnological processes. Subsequent attempts to isolate new thermophilic organisms have been very successful. Moreover, these results, in combination with much-improved techniques for studying the phylogeny of microorganisms, have renewed interest in the evolution of microbes and the early development of life.     

Compatible and incompetent Paxillus involutus isolates for ectomycorrhiza formation in vitro with poplar (Populus x canescens) differ in H2O2 production

Abstract: Isolates of Paxillus involutus (Batsch) Fr. collected from different hosts and environmental conditions were screened for their ability to form ectomycorrhizal symbiosis with hybrid poplar P. × canescens ( = Populus tremula L. × P. alba) in vitro. The ability to form ectomycorrhiza varied between the fungal isolates and was not correlated with the growth rate of the fungi on agar-based medium. The isolate MAJ, which was capable of mycorrhiza synthesis under axenic conditions, and the incompetent isolate NAU were characterized morphologically and anatomically. MAJ formed a typical hyphal mantle and a Hartig net, whereas NAU was not able to penetrate the host cell walls and caused thickenings of the outer cell walls of the host. MAJ, but not NAU, displayed strong H₂O₂ accumulation in the outer hyphal mantle. Increases in H₂O₂ in the outer epidermal walls and adjacent hyphae of the incompetent isolate were moderate. No increases of H₂O₂ in response to the mycobionts were found inside roots. Suggested functions of H₂O₂ production in the outer hyphal mantle of the compatible interaction are: growth regulation of the host's roots, defence against other invading microbes, or increasing plant-innate immunity. The system established here for P. × canescens compatible and incompetent fungal associations will be useful to take advantage of genomic information now available for poplar to study tree-fungal interactions at the molecular and physiological level.     

Proton Irradiation Facility and space radiation monitoring at the Paul Scherrer Institute

The Proton Irradiation Facility (PIF) has been designed and constructed, in cooperation between Paul Scherrer Institute (PSI) and European Space Agency (ESA), for terrestrial proton testing of components and materials for spacecraft. Emphasis has been given to generating realistic proton spectra encountered by space-flights at any potential orbit. The facility, designed in a user-friendly manner, can be readily adapted to the individual requirements of experimenters. It is available for general use serving also in testing of radiation monitors and for proton experiments in different scientific disciplines. The Radiation Environment Monitor REM has been developed for measurements of the spacecraft radiation conditions. Two instruments were launched into space, one into a Geo-stationary Transfer Orbit on board of the STRV-1b satellite and one into a Low Earth Orbit on the Russian MIR station. The next generation of monitors (SREMs--Standard REMs) is currently under development in partnership of ESA, PSI and Contraves-Space. They will operate both as minimum intrusive monitors, which provide radiation housekeeping data and alert the spacecraft when the radiation level crosses allowed limits and as small scientific devices measuring particle spectra and fluxes. Future missions as e.g. INTEGRAL, STRV-1c and PROBA will be equipped with new SREMs.     

Isolation of highly copper‐tolerant fungi from the smelter of the Naganobori copper mine,an historic mine in Japan

Aims: Copper is a critical metal of modern industry, and is the most widespread heavy metal contaminant in wastewater. Therefore, isolation of copper‐tolerant microbes having the potential as biosorbent is fascinating not only from an environmental microbiology, but also from a biotechnology view point. In this study, we attempted to isolate highly copper‐tolerant microbes from soil samples of the Nabanobori copper mine, the oldest mine in Japan. Methods and Results: As a result of an enrichment culture, two fungal strains were isolated from soil of the smelter remains. The isolates could grow in a maximum of 200 mmol l^?l Cu²⁺, and grew under a wide pH range. The Cu²⁺‐binding capacity of nontreated biomass of the isolates was around 35 mg Cu²⁺ g^?1‐biomass. Analysis of 18S rDNA suggested that the isolates belong to the Aspergillus/Penicillium clade, but they represented a distinct lineage against known neighbours. Conclusion: The isolates were highly copper‐tolerant, and their Cu²⁺‐binding capacity was comparable to well‐studied fungal sorbents. The isolates were implied as novel species. Soil of the historic old mine under weather‐beaten conditions might be a suitable source for metal‐tolerant microbes. Significance and Impact of the Study: The present results advance our understanding of metal‐tolerant microbes, and offer a new tool for both environmental control and metal recovery operations.     

淡豆豉对人体肠道六种常住菌的调节作用

目的初探淡豆豉对人体肠道6种常住菌的调节作用。方法利用选择性培养基从人的粪便中分离培养肠杆菌、肠球菌、双歧杆菌、乳杆菌、产气荚膜梭菌和脆弱拟杆菌6种人体肠道常住菌。将高、中和低浓度淡豆豉药液加入选择性培养基中,以不加药液的培养基作为空白对照,根据各菌种培养条件分别于厌氧或好氧条件下培养,然后进行菌落计数。结果与空白对照相比,加药培养基脆弱拟杆菌增长20.00%以上;而其他5种菌的生长均被不同程度的抑制,其中对乳杆菌和肠球菌抑制作用最强,加药培养基上这2种菌均不生长;50.00%浓度药液对产气荚膜梭菌抑制率为32.81%;20.00%浓度药液对肠杆菌完全抑制,但随着药液浓度增大抑制作用减弱,50.00%和70.00%浓度药液对肠杆菌的抑制率分别为53.83%和22.11%;低、中和高浓度药液对双歧杆菌的抑制率分别为17.07%、17.83%和17.84%,差异无统计学意义。结论淡豆豉对人体6种肠道常住菌具有不同程度的调节作用。     

Aerobic reduction of perchlorate by bacteria isolated in Kerala, South India

Possibility of perchlorate reduction by microbes raises hope for an eco-friendly mode of degradation of this toxic rocket fuel. This study reports 3 isolates (A1, A2 and A3) capable of molybdenum-independent degradation of perchlorate under aerobic conditions. The rate of degradation was the highest when perchlorate concentration was 17 mM, and then 3.2 mM, 4.7 mM and 4.1 mM of perchlorate was reduced by isolates A1, A2 and A3 (respectively) after 72 h at 28°C under aerobic conditions. Presence of perchlorate at a concentration higher than 17 mM resulted in some inhibition of perchlorate reduction. 16S ribosomal RNA gene analysis revealed isolate A1 to bePseudomonas stutzeri (Proteobacteria) while isolates A2 ad A3 where found to belong to the genusArthrobacter (Actinobacteria). The study, apart from demonstrating ribotyping as a rapid method of identification of economically important soil microbes, also raised prospects for using artificial consortia for environmental degradation of perchlorate, without apparent domination ofDechloromonas spp. (a group of microbes known for perchlorate remediation in the environment).     

Visualization of yeast single-cells on fabric surface with a fluorescent glucose and their isolation for culture

An ultra-deep focusing range (UDF) fluorescent microscope system has been combined with a micromanipulation system to develop a viable cell detection-identification system applicable to microbes on environmental surfaces and products. Candida albicans yeast cells on a fabric sample surface were viably stained with a fluorescent glucose derivative, 2-[N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino]-2-deoxy glucose (2-NBDG) and detected with a UDF fluorescent microscope. Visualized single-cells of C. albicans were picked in a glass microcapillary and transferred onto an agar medium. After the culture, the colony was assayed for DNA sequence to identify the isolate. This demonstrates a potential application to the study of unknown environmental microorganisms.     

瘤胃中木质纤维素降解菌及降解酶基因的研究进展

摘要：反刍动物瘤胃是公认的木质纤维素高效降解的天然反应器,对瘤胃微生物的研究成为开发生物能源的热点领域之一。其研究手段已经从传统的依赖分离培养从瘤胃中获得木质纤维素降解菌,并对降解菌中的木质纤维素降解酶逐一分析,发展到通过基因组/元基因组技术,直接从瘤胃中发现获得大量新的木质纤维素降解酶基因/基因簇,进而探讨其降解的分子机理。已有的研究结果表明,瘤胃微生物降解木质纤维素的过程非常复杂,其中涉及到大量不同种类的微生物、酶及基因/基因簇,随着新分析技术的建立和完善,对这些微生物、酶和基因的研究已取得了诸多进展。本论文综述报道了近期有关该方向的研究进展。     

Rhizoremediation of lindane by root‐colonizing Sphingomonas

We used a two‐step enrichment approach to isolate root‐colonizing hexachlorocyclohexane (HCH)‐degrading microorganisms. The first step consists of the use of classical liquid enrichment to isolate γ‐HCH degraders. The γ‐HCH‐degrading microbes were attached in mass to corn seeds sown in soil with γ‐HCH, and after plant development we rescued bacteria growing on root tips. Bacteria were then subjected to a second enrichment round in which growth on liquid medium with γ‐HCH and inoculation of corn seeds were repeated. We then isolated bacteria on M9 minimal medium with γ‐HCH from root tips. We were able to isolate four Sphingomonas strains, all of which degraded α‐, β‐, γ‐ and δ‐HCH. Two of the strains were particularly good colonizers of corn roots, reaching high cell density in vegetated soil and partly removing γ‐HCH. In contrast, these bacteria performed poorly in unplanted soils. This study supports the hypothesis that the removal of persistent toxic chemicals can be accelerated by combinations of plants and bacteria, a process generally known as rhizoremediation.     

Sponge-specific clusters revisited: a comprehensive phylogeny of sponge-associated microorganisms

Marine sponges often contain diverse and abundant communities of microorganisms including bacteria, archaea and eukaryotic microbes. Numerous 16S rRNA-based studies have identified putative 'sponge-specific' microbes that are apparently absent from seawater and other (non-sponge) marine habitats. With more than 7500 sponge-derived rRNA sequences (from clone, isolate and denaturing gradient gel electrophoresis data) now publicly available, we sought to determine whether the current notion of sponge-specific sequence clusters remains valid. Comprehensive phylogenetic analyses were performed on the 7546 sponge-derived 16S and 18S rRNA sequences that were publicly available in early 2010. Overall, 27% of all sequences fell into monophyletic, sponge-specific sequence clusters. Such clusters were particularly well represented among the Chloroflexi, Cyanobacteria, 'Poribacteria', Betaproteobacteria and Acidobacteria, and in total were identified in at least 14 bacterial phyla, as well as the Archaea and fungi. The largest sponge-specific cluster, representing the cyanobacterium 'Synechococcus spongiarum', contained 245 sequences from 40 sponge species. These results strongly support the existence of sponge-specific microbes and provide a suitable framework for future studies of rare and abundant sponge symbionts, both of which can now be studied using next-generation sequencing technologies.