Isolation of Two Radiation Resistant and Desiccation Tolerant Bacteria, <Emphasis Type="Italic">Modestobacter</Emphasis> sp. A2 and <Emphasis Type="Italic">Maritalea</Emphasis> sp. B9, from Gandom Beryan Hill in the Lut Desert of Iran

Although dryland ecosystems are the most abundant terrestrial biomes on the Earth, relatively little is known about their microbial diversity and potential metabolic activities. Therefore, the bacterial diversity of the Lut Desert in Iran has been remained largely obscure. In this study, ionizing radiation resistant bacteria from arid Gandom Beryan region was investigated by a culture-dependent method. After exposing the soil and surface sand samples to different periods of dehydration in a desiccator containing silica gel, two nonendospore- forming bacterial isolates were recovered by plating on R2A and TSA agar media and then subjected to a desiccation and ionizing radiation resistance assay. The isolates A2 and B9 were still recovered after 8 weeks in a desiccator containing silica gel and were moderately resistant to gamma radiation with a D10 value between 2 and 4 kGy. Strains A2 and B9 were affiliated with Modestobacter muralis MDVD1^T (99.7% similarity) and Maritalea mobilis E6^T (97.3% similarity) respectively, using 16S rRNA gene sequence analysis. This is the first report of radiation resistant bacteria which belongs to the genus Maritalea.     

Complete genome sequence of Deinococcus maricopensis type strain (LB-34)

Deinococcus maricopensis (Rainey and da Costa 2005) is a member of the genus Deinococcus, which is comprised of 44 validly named species and is located within the deeply branching bacterial phylum Deinococcus-Thermus. Strain LB-34(T) was isolated from a soil sample from the Sonoran Desert in Arizona. Various species of the genus Deinococcus are characterized by extreme radiation resistance, with D. maricopensis being resistant in excess of 10 kGy. Even though the genomes of three Deinococcus species, D. radiodurans, D. geothermalis and D. deserti, have already been published, no special physiological characteristic is currently known that is unique to this group. It is therefore of special interest to analyze the genomes of additional species of the genus Deinococcus to better understand how these species adapted to gamma- or UV ionizing-radiation. The 3,498,530 bp long genome of D. maricopensis with its 3,301 protein-coding and 66 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Geomicrobiology of high-level nuclear waste-contaminated vadose sediments at the hanford site, washington state

Sediments from a high-level nuclear waste plume were collected as part of investigations to evaluate the potential fate and migration of contaminants in the subsurface. The plume originated from a leak that occurred in 1962 from a waste tank consisting of high concentrations of alkali, nitrate, aluminate, Cr(VI), (137)Cs, and (99)Tc. Investigations were initiated to determine the distribution of viable microorganisms in the vadose sediment samples, probe the phylogeny of cultivated and uncultivated members, and evaluate the ability of the cultivated organisms to survive acute doses of ionizing radiation. The populations of viable aerobic heterotrophic bacteria were generally low, from below detection to approximately 10(4) CFU g(-1), but viable microorganisms were recovered from 11 of 16 samples, including several of the most radioactive ones (e.g., >10 microCi of (137)Cs/g). The isolates from the contaminated sediments and clone libraries from sediment DNA extracts were dominated by members related to known gram-positive bacteria. Gram-positive bacteria most closely related to Arthrobacter species were the most common isolates among all samples, but other phyla high in G+C content were also represented, including Rhodococcus and Nocardia. Two isolates from the second-most radioactive sample (>20 microCi of (137)Cs g(-1)) were closely related to Deinococcus radiodurans and were able to survive acute doses of ionizing radiation approaching 20 kGy. Many of the gram-positive isolates were resistant to lower levels of gamma radiation. These results demonstrate that gram-positive bacteria, predominantly from phyla high in G+C content, are indigenous to Hanford vadose sediments and that some are effective at surviving the extreme physical and chemical stress associated with radioactive waste.     

Effect of soil bacteria on hyphal growth of the arbuscular mycorrhizal fungus Glomus claroideum

The effect of 46 bacterial strains isolated from tilled and non-tilled soils collected at 3 localities on the growth of intraradical hyphae of the arbuscular mycorrhizal (AM) fungusGlomus claroideum was demonstrated. A larger number of stimulatory bacterial isolates was obtained from tilled soils, but the bacteria showing the strongest stimulation of hyphal growth were isolated from a soil that had not been cultivated. Isolates obtained from hyphae of AM fungi showed no substantial stimulatory effects, but produced more uniform effects on hyphal growth than the isolates of bacteria obtained from soil. Bacterial cenoses present in 3 different soils differ significantly in their effects on AM fungi.     

The prokaryotic diversity of biological soil crusts in the Sonoran Desert (Organ Pipe Cactus National Monument, AZ)

We studied prokaryotic community structure and composition in biological soil crusts (BSCs) from the Sonoran Desert, and their variability over space and time, using statistically analyzed, PCR-based molecular surveys of environmental 16S rRNA genes. Four sites, tens of km apart, were sampled, 3 times over a 1 year period, collecting 10 duplicate samples every 50 m in each site. Denaturing gradient gel electrophoresis (DGGE) revealed communities much less diverse than those of typical soil assemblages, displaying dominance of some bacterial types. No differences in crust microbial diversity or composition were detected between crusts under plant canopies and those in plant interspaces, indicating a likely crust independence from higher plant resources. However, statistically significant variability with space and time could be detected, and samples within a site were more similar than samples between sites. Both temporal and spatial variability in community composition involved non-dominant members of the community. Extensive sequencing and phylogenetic analysis revealed a large array of bacterial types, many novel. The most common included members of Cyanobacteria, Proteobacteria, Actinobacteria and Acidobacteria. Bacteriodetes, Chloroflexi and Gemmatimonadetes were not seen in high numbers, but were present in all sites, and Deinococci were also detected. Archaea were present, but as minor components. Sonoran BSC communities were distinct in rough compositional character from those in bulk arid soils or agricultural soils, and contained reoccurring, uncultured microbes.     

一株新的耐辐射菌Deinococcus guangxiensis sp.nov.的分离鉴定及耐辐射特性分析

摘要：【目的】从广西大学辐射中心辐射源附近被常年辐射的水样中分离并鉴定出新的耐辐射菌株,并对其耐辐射特性进行研究。【方法】通过GBM培养基分离培养得到一株新的耐辐射菌株,命名为WGR700T。应用生理生化试验,脂肪酸含量,(G+C) mol％含量测定以及16S rRNA序列同源性分析等方法对菌株进行鉴定,同时对WGR700T的耐辐射特性进行分析。【结果】菌株WGR700T为革兰氏阴性,杆状,没有鞭毛,不能运动,厌氧并能产生红色素。最佳生长温度和PH分别为37℃和pH7.0,主要的呼吸醌是MK-8,细胞壁内还有鸟氨酸,主要脂肪酸为16:1ω7c, 16:0, 15:1ω6c, iso-15:0和 iso-17:0。G+C含量为64.7mol%。菌株WGR700T具有很强的UV(>728 J/m2)和电离辐射抗性(D10 = 9.8 kGy)。菌株WGR700T和奇异球菌属（Deinococcus）内其它菌种16S rRNA有很高的相似性（87.1-95.6%）。【结论】根据16S rRNA及生理生化特征区别,菌株WGR700T应是奇异球菌属的一个新种,命名为Deinococcus guangxiensis sp. nov. 模式菌株为WGR700T(= CGMCC1.7045T =CICC 10360T = JCM 15082T)。     

Effects of altered temperature and precipitation on desert protozoa associated with biological soil crusts

Biological soil crusts are diverse assemblages of bacteria, cyanobacteria, algae, fungi, lichens, and mosses that cover much of arid land soils. The objective of this study was to quantify protozoa associated with biological soil crusts and test the response of protozoa to increased temperature and precipitation as is predicted by some global climate models. Protozoa were more abundant when associated with cyanobacteria/lichen crusts than with cyanobacteria crusts alone. Amoebae, flagellates, and ciliates originating from the Colorado Plateau desert (cool desert, primarily winter precipitation) declined 50-, 10-, and 100-fold, respectively, when moved in field mesocosms to the Chihuahuan Desert (hot desert, primarily summer rain). However, this was not observed in protozoa collected from the Chihuahuan Desert and moved to the Sonoran desert (hot desert, also summer rain, but warmer than Chihuahuan Desert). Protozoa in culture began to encyst at 37 degrees C. Cysts survived the upper end of daily temperatures (37-55 degrees C), and could be stimulated to excyst if temperatures were reduced to 15 degrees C or lower. Results from this study suggest that cool desert protozoa are influenced negatively by increased summer precipitation during excessive summer temperatures, and that desert protozoa may be adapted to a specific desert's temperature and precipitation regime.     

Effect of natamycin on the enumeration, genetic structure and composition of bacterial community isolated from soils and soybean rhizosphere

Natamycin is commonly used to control fungal growth on agar media used for bacterial enumeration or strain isolation. However, there is no conclusive report on the possible effect of this antibiotic on bacterial growth or on the diversity of the recovered soil bacteria. Therefore, the possible effects of natamycin on the numbers of bacteria isolated at 12 degrees C from three different soils and soybean rhizosphere soil were investigated using natamycin concentrations ranging from 0 to 200 mg l(-1). Our results demonstrate that natamycin concentrations, which inhibit the growth of fungi on the media, have a small but significant inhibitory effect on the number of bacterial colony forming units. A natamycin concentration of 50-200 mg l(-1) is required for an efficient control of fungal growth on media in our experimental conditions depending on the soil type. Bacterial community structure was assessed on culturable cells (cells washed from enumeration plates: plate-wash approach) obtained at 12 degrees C from soybean rhizosphere soil by performing Ribosomal Intergenic Spacer Analysis (RISA) fingerprinting. We demonstrate that all natamycin concentrations used alter the structure of the recovered, culturable bacterial community, compared to control without natamycin. Using ARDRA (amplification of the 16S rDNA gene and restriction analysis) genotyping of individual isolates, some differences were observed between the bacterial isolates obtained in the presence or absence of natamycin. Bacterial isolates recovered in the presence of natamycin are more tolerant (maximal growth rate and lag phase) to this compound than those isolated without natamycin, indicating a possible selection of resistant strains. Therefore, high concentration of natamycin cannot be used for isolation of bacterial strains with the aim of studying biodiversity and could bias a selection of strains for practical applications.     

Diversity of culturable actinomycetes in hyper-arid soils of the Atacama Desert,Chile

The Atacama Desert presents one of the most extreme environments on Earth and we report here the first extensive isolations of actinomycetes from soils at various locations within the Desert. The use of selective isolation procedures enabled actinomycetes to be recovered from arid, hyper-arid and even extreme hyper-arid environments in significant numbers and diversity. In some cases actinomycetes were the only culturable bacteria to be isolated under the conditions of this study. Phylogenetic analysis and some phenotypic characterisation revealed that the majority of isolates belonged to members of the genera Amycolatopsis, Lechevalieria and Streptomyces, a high proportion of which represent novel centres of taxonomic variation. The results of this study support the view that arid desert soils constitute a largely unexplored repository of novel bacteria, while the high incidence of non-ribosomal peptide synthase genes in our isolates recommend them as promising material in screening for new bioactive natural products.     

Sensitivity of planktonic and biofilm-associated Salmonella spp. to ionizing radiation

Salmonella enterica forms biofilms that are relatively resistant to chemical sanitizing treatments. Ionizing radiation has been used to inactivate Salmonella on a variety of foods and contact surfaces, but the relative efficacy of the process against biofilm-associated cells versus free-living planktonic cells is not well documented. The radiation sensitivity of planktonic or biofilm-associated cells was determined for three food-borne-illness-associated isolates of Salmonella. Biofilms were formed on sterile glass slides in a coincubation apparatus, using inoculated tryptic soy broth, incubated at 37 degrees C for 48 h. Resulting biofilms were 18 to 24 microm in height as determined by confocal scanning laser microscopy. The planktonic and biofilm cultures were gamma irradiated to doses of 0.0 (control), 0.5, 1.0, 1.5, 2.0 and 2.5 kGy. The D(10) value (the dose of radiation required to reduce a population by 1 log(10), or 90%) was calculated for each isolate-culture based on surviving populations at each radiation dose. The D(10) values of S. enterica serovar Anatum were not significantly (P < 0.05) different for biofilm-associated (0.645 kGy) and planktonic (0.677 kGy) cells. In contrast, the biofilm-associated cells of S. enterica serovar Stanley were significantly more sensitive to ionizing radiation than the respective planktonic cells, with D(10) values of 0.531 and 0.591 kGy, respectively. D(10) values of S. enterica serovar Enteritidis were similarly reduced for biofilm-associated (0.436 kGy) versus planktonic (0.535 kGy) cells. The antimicrobial efficacy of ionizing radiation is therefore preserved or enhanced in treatment of biofilm-associated bacteria.     

Deciphering peculiar protein-protein interacting modules in Deinococcus radiodurans

Interactomes of proteins under positive selection from ionizing-radiation-resistant bacteria (IRRB) might be a part of the answer to the question as to how IRRB, particularly Deinococcus radiodurans R₁ (Deira), resist ionizing radiation. Here, using the Database of Interacting Proteins (DIP) and the Protein Structural Interactome (PSI)-base server for PSI map, we have predicted novel interactions of orthologs of the 58 proteins under positive selection in Deira and other IRRB, but which are absent in IRSB. Among these, 18 domains and their interactomes have been identified in DNA checkpoint and repair; kinases pathways; energy and nucleotide metabolisms were the important biological processes that were found to be involved. This finding provides new clues to the cellular pathways that can to be important for ionizing-radiation resistance in Deira.     

Comparison of soil bacterial communities in rhizospheres of three plant species and the interspaces in an arid grassland

Soil bacteria are important contributors to primary productivity and nutrient cycling in arid land ecosystems, and their populations may be greatly affected by changes in environmental conditions. In parallel studies, the composition of the total bacterial community and of members of the Acidobacterium division were assessed in arid grassland soils using terminal restriction fragment length polymorphism (TRF, also known as T-RFLP) analysis of 16S rRNA genes amplified from soil DNA. Bacterial communities associated with the rhizospheres of the native bunchgrasses Stipa hymenoides and Hilaria jamesii, the invading annual grass Bromus tectorum, and the interspaces colonized by cyanobacterial soil crusts were compared at three depths. When used in a replicated field-scale study, TRF analysis was useful for identifying broad-scale, consistent differences in the bacterial communities in different soil locations, over the natural microscale heterogeneity of the soil. The compositions of the total bacterial community and Acidobacterium division in the soil crust interspaces were significantly different from those of the plant rhizospheres. Major differences were also observed in the rhizospheres of the three plant species and were most apparent with analysis of the Acidobacterium division. The total bacterial community and the Acidobacterium division bacteria were affected by soil depth in both the interspaces and plant rhizospheres. This study provides a baseline for monitoring bacterial community structure and dynamics with changes in plant cover and environmental conditions in the arid grasslands.     

Viability, diversity and composition of the bacterial community in a high Arctic permafrost soil from Spitsbergen, Northern Norway

The viable and non-viable fractions of the bacterial community in a 2347-year-old permafrost soil from Spitsbergen were subjected to a comprehensive investigation using culture-independent and culture-dependent methods. LIVE/DEAD BacLight staining revealed that 26% of the total number of bacterial cells were viable. Quantitatively, aerobic microcolonies, aerobic colony-forming units and culturable anaerobic bacteria comprised a minor fraction of the total number of viable bacteria, which underlines the necessity for alternative cultivation approaches in bacterial cryobiology. Sulfate reduction was detected at temperatures between -2 degrees C and 29 degrees C while methanogenesis was not detected. Bacterial diversity was high with 162 operational taxonomic units observed from 800 16S rDNA clone sequences. The 158 pure cultures isolated from the permafrost soil affiliated with 29 different bacterial genera, the majority of which have not previously been isolated from permafrost habitats. Most of the strains isolated were affiliated to the genera Cellulomonas and Arthrobacter and several of the pure cultures were closely related to bacteria reported from other cryohabitats. Characterization of viable bacterial communities in permafrost soils is important as it will enable identification of functionally important groups together with the as yet undescribed adaptations that bacteria have evolved for surviving subzero temperatures for millennia.     

塔里木盆地荒漠盐碱生境嗜盐碱细菌的初步研究

为了探索塔里木盆地荒漠盐碱生境嗜（耐）盐碱细菌的分离方法,采用纯培养技术探讨了不同土壤预处理方法、盐度及不同分离培养基对不同盐度土壤中嗜（耐）盐碱细菌分离效果的影响。结果表明：高盐土壤嗜（耐）盐碱细菌的多样性高于中度盐分和低度盐分的土壤,而总菌落数则相反;半量的Horikoshi I（NaCl 10％～15％）为3种土样最佳的分离培养基,碱性复合培养基和高盐碱培养基A次之;分离嗜（耐）盐碱细菌以获得资源为主要目的时,富集培养法最佳。以反映土壤嗜（耐）盐碱细菌生态分布而言,用土壤悬液法;塔里木盆地嗜（耐）盐碱细菌生长盐浓度及pH值范围较宽,最适生长盐浓度为10％左右,pH值多为8—10左右。分离到的120株嗜（耐）盐碱细菌中,有33株为嗜盐碱细菌,占分离菌株的27．5％。     

Geomicrobiology of High-Level Nuclear Waste-Contaminated Vadose Sediments at the Hanford Site, Washington State

Sediments from a high-level nuclear waste plume were collected as part of investigations to evaluate the potential fate and migration of contaminants in the subsurface. The plume originated from a leak that occurred in 1962 from a waste tank consisting of high concentrations of alkali, nitrate, aluminate, Cr(VI), ¹³⁷Cs, and ⁹⁹Tc. Investigations were initiated to determine the distribution of viable microorganisms in the vadose sediment samples, probe the phylogeny of cultivated and uncultivated members, and evaluate the ability of the cultivated organisms to survive acute doses of ionizing radiation. The populations of viable aerobic heterotrophic bacteria were generally low, from below detection to ~10⁴ CFU g⁻¹, but viable microorganisms were recovered from 11 of 16 samples, including several of the most radioactive ones (e.g., >10 μCi of ¹³⁷Cs/g). The isolates from the contaminated sediments and clone libraries from sediment DNA extracts were dominated by members related to known gram-positive bacteria. Gram-positive bacteria most closely related to Arthrobacter species were the most common isolates among all samples, but other phyla high in G+C content were also represented, including Rhodococcus and Nocardia. Two isolates from the second-most radioactive sample (>20 μCi of ¹³⁷Cs g⁻¹) were closely related to Deinococcus radiodurans and were able to survive acute doses of ionizing radiation approaching 20 kGy. Many of the gram-positive isolates were resistant to lower levels of gamma radiation. These results demonstrate that gram-positive bacteria, predominantly from phyla high in G+C content, are indigenous to Hanford vadose sediments and that some are effective at surviving the extreme physical and chemical stress associated with radioactive waste.     

Effect of biological soil crusts on soil elemental concentrations: implications for biogeochemistry and as traceable biosignatures of ancient life on land

Biological soil crusts (BSCs) are topsoil biosedimentary structures built by photosynthetic microbes commonly found today on arid soils. They play a role in soil stabilization and the fertility of arid lands, and are considered modern analogues of ancient terrestrial microbial communities. We determined the concentrations of four biogenic and 21 other elements, mostly metals, in surface soils that hosted BSCs, in the soils underneath those crusts, and in proximate but non-crusted surface soils. The samples were from six sites in the Colorado Plateau highlands and the Sonoran Desert lowlands. In spite of the variability in climate and geologic setting, we found statistically significant overall trends of enrichment in biogenic elements and depletion in non-biogenic elements when BSCs were compared with non-crusted soils. The differences between crusted and non-crusted soils were statistically significant at ∼95% confidence for C, N (enrichments) and for Ca, Cr, Mn, Cu, Zn, As, and Zr (depletions). These trends are best explained by the activity of microbes. As expected, no differences in the concentrations of C, N, P, and S were detected between the soils underneath the crusts and the non-crusted soils, but the former showed depletion of non-biogenic elements, indicating that the leaching effect of crust microbes extends downward in the soil. These patterns speak to the need for a sustained input of allochthonous material, possibly dust, to maintain BSC fertility. These elemental patterns can be considered a biosignature that may be preserved in the rock record and might help identify ancient microbial communities on land.     

Historical forest disturbance mediates soil microbial community responses to drought

Despite the abundance of studies demonstrating the effects of drought on soil microbial communities, the role of land use legacies in mediating these drought effects is unclear. To assess historical land use influences on microbial drought responses, we conducted a drought-rewetting experiment in soils from two adjacent and currently forested watersheds with distinct land use histories: an undisturbed ‘reference’ site and a ‘disturbed’ site that was clear-cut and converted to agriculture ~60 years prior. We incubated intact soil cores at either constant moisture or under a drought-rewet treatment and characterized bacterial and fungal communities using amplicon sequencing throughout the experiment. Bacterial alpha diversity decreased following drought-rewetting while fungal diversity increased. Bacterial beta diversity also changed markedly following drought-rewetting, especially in historically disturbed soils, while fungal beta diversity exhibited little response. Additionally, bacterial beta diversity in disturbed soils recovered less from drought-rewetting compared with reference soils. Disturbed soil communities also exhibited notable reductions in nitrifying taxa, increases in putative r-selected bacteria, and reductions in network connectivity following drought-rewetting. Overall, our study reveals historical land use to be important in mediating responses of soil bacterial communities to drought, which will influence the ecosystem-scale trajectories of these environments under ongoing and future climate change.     

Ultraviolet irradiation of soil samples as a model of the effect of stress factors on bacterial diversity in soil ecosystem

UV irradiation is proposed for use in studying the effect of radioactive irradiation, since radioresistant bacteria are, as a rule, resistant to UV, and the mechanisms of repair of cell damage induced by UV and ionizing radiation are similar. It was found that the total number of bacteria and the number of dominant species in soil samples exposed to UV radiation decreased, indicating the unfavorable effect of UV radiation on bacterial diversity in soil ecosystems. The percentage of cells of bacteria belonging to dominant species varied significantly depending on the intensity of UV irradiation. It can be inferred that long-term irradiation of soils must impair the stability of soil ecosystems, a phenomenon that was indeed observed in the zone around the Chernobyl Nuclear Power Plant. At the same time, the UV irradiation of soil samples made it possible to reveal minor species, primarily UV-resistant pigmented bacteria. UV irradiation can probably be used as a selective factor for the isolation of radioresistant species.     

Patterns of diversity for fungal assemblages of biological soil crusts from the southwestern United States

Molecular methodologies were used to investigate fungal assemblages of biological soil crusts (BSCs) from arid lands in the southwestern United States. Fungal diversity of BSCs was assessed in a broad survey that included the Chihuahuan and Sonoran deserts as well as the Colorado Plateau. At selected sites samples were collected along kilometer-scale transects, and fungal community diversity and composition were assessed based on community rRNA gene fingerprinting using PCR-denaturing gradient gel electrophoresis (DGGE). Individual phylotypes were characterized through band sequencing. The results indicate that a considerable diversity of fungi is present within crusted soils, with higher diversity being recovered from more successionally mature BSCs. The overwhelming majority of crust fungi belong to the Ascomycota, with the Pleosporales being widespread and frequently dominant. Beta diversity patterns of phylotypes putatively representing dominant members of BSC fungal communities suggest that these assemblages are specific to their respective geographic regions of origin.     

The Effect of Resource Islands on Abundance and Diversity of Bacteria in Arid Soils

Bacteria and nutrients were determined in upper soil samples collected underneath and between canopies of the dominant perennial in each of three sites along a steep precipitation gradient ranging from the Negev desert in the south of Israel to a Mediterranean forest in the north. Bacterial abundance, monitored by phospholipid fatty acid analysis, was significantly higher under the shrub canopy (compared to barren soils) in the arid and semi-arid sites but not in the Mediterranean soils. Bacterial community composition, determined using terminal restriction fragment length polymorphism and clone libraries, differed according to the sample’s origin. Closer examination revealed that in the arid and semi-arid sites, α-Proteobacteria are more abundant under the shrub canopy, while barren soils are characterized by a higher abundance of Actinobacteria. The bacterial communities in the Mediterranean soils were similar in both patch types. These results correspond to the hypothesis of “resource islands”, suggesting that shrub canopies provide a resource haven in low-resource landscapes. Yet, a survey of the physicochemical parameters of inter- and under-shrub soils could not attribute the changes in bacterial diversity to soil moisture, organic matter, or essential macronutrients. We suggest that in the nutrient-poor soils of the arid and semi-arid sites, bacteria occupying the soil under the shrub canopy may have longer growth periods under favorable conditions, resulting in their increased biomass and altered community composition.