The stratified microbial community at Laguna Figueroa, Baja California, Mexico - A possible model for prephanerozoic laminated microbial communities preserved in cherts
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Stolz, J. F.↗
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Results for “microbial communities”
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Environmental factors driving spatial heterogeneity in desert halophile microbial communities
Spatial heterogeneity in microbial communities is observed in all-natural ecosystems and can stem from both adaptations to local environmental conditions as well as stochastic processes. Extremophile microbial communities inhabiting evaporitic halite nodules (salt rocks) in the Atacama Desert, Chile, are a good model ecosystem for investigating factors leading to microbiome heterogeneity, due to their diverse taxonomic composition and the spatial segregation of individual nodules. We investigated the abiotic factors governing microbiome composition across different spatial scales, allowing for insight into the factors that govern halite colonization from regional desert-wide scales to micro-scales within individual nodules. We found that water availability and community drift account for microbiome assembly differently at different distance scales, with higher rates of cell dispersion at the smaller scales resulting in a more homogenous composition. This trend likely applies to other endoliths, and to non desert communities, where dispersion between communities is limited. At the intra-nodule scales, a light availability gradient was most important in determining the distribution of microbial taxa despite intermixing by water displacement via capillary action.
microbiome extremophile, desert, heterogeneity, Me↗
The Influence of Ecological Isolation on the Structural and Functional Stability of Complex Microbial Communities
To help understand how the behavior of microorganisms and microbial communities in insular space habitats may differ from the behavior of these groups on Earth, long-term incubations (100+ days) were conducting using wastewater bioreactors (batch fed) designed to mimic "closed" and "open" ecological systems. The issue of immigration was considered, and the goal of the research was to determine whether the stability of microbial communities in space is reduced due to their prolonged isolation. Bioreactors were established by inoculating flasks of sterile synthetic wastewater with the microbial community obtained from a local treatment facility; each day, one-third of the medium in the flask was replaced with an equal volume of sterile artificial wastewater. Flasks were divided into two treatments: "closed" and "open" to recruitment of additional microorganisms. "Closed" flasks were maintained as described above, while the medium used to feed the "open" flasks was supplemented daily with a small amount of raw sewage (which provided a continuous source of new potential community members). Significant differences in microbial community structure and function developed in the two sets of communities, and the results suggest that the open community was more stable and better able to adjust to changing environmental conditions. Each community's resistance to environmental (temperature fluctuations) and biological stresses (starvation and invasion by an opportunistic pathogen Pseudomonas aeruginosa) was monitored. Experiments were also conducted to determine whether the effect of isolation changes depending on the microbial communities' initial diversity or composition; communities with a low(er) initial diversity were less stable. Overall, the results indicate that isolation will be an important factor influencing the activity of microbial communities on board spacecraft. A possible way of mitigating these effects would be to include communities with high initial diversity or to periodically re-inoculate the systems using diverse inocula transported from Earth.
Franklin, R. B.↗
Does iron inhibit cryptoendolithic microbial communities?
Photosynthetic activity of three cryptoendolithic microbial communities was studied under controlled conditions in the laboratory. In two of these communities, the dominant organisms were lichens, collected from Linnaeus Terrace and from Battleship Promontory. The third community, dominated by cyanobacteria, was collected from Battleship Promontory. Both sites are in the ice-free valleys of southern Victoria Land. Previous efforts have shown how physical conditions can influence metabolic activity in endolithic communities (Kappen and Friedmann 1983; Kappen, Friedmann, and Garty 1981; Vestal, Federle, and Friedmann 1984). Biological activity can also be strongly influenced by the chemical environment. Inorganic nutrients such as nitrate, ammonia, and phosphate are often limiting factors, so their effects on photosynthetic carbon-14 bicarbonate incorporation were investigated. Iron and manganese are two metals present in Linnaeus Terrace and Battleship Promontory sandstones, and their effects on photosynthesis were also studied. The results may add to our understanding of biogeochemical interactions within this unique microbial community.
Non-NASA Center↗
Composition and physiological profiling of sprout-associated microbial communities
The native microfloras of various types of sprouts (alfalfa, clover, sunflower, mung bean, and broccoli sprouts) were examined to assess the relative effects of sprout type and inoculum factors (i.e., sprout-growing facility, seed lot, and inoculation with sprout-derived inocula) on the microbial community structure of sprouts. Sprouts were sonicated for 7 min or hand shaken with glass beads for 2 min to recover native microfloras from the surface, and the resulting suspensions were diluted and plated. The culturable fraction was characterized by the density (log CFU/g), richness (e.g., number of types of bacteria), and diversity (e.g., microbial richness and evenness) of colonies on tryptic soy agar plates incubated for 48 h at 30 degrees C. The relative similarity between sprout-associated microbial communities was assessed with the use of community-level physiological profiles (CLPPs) based on patterns of utilization of 95 separate carbon sources. Aerobic plate counts of 7.96 +/- 0.91 log CFU/g of sprout tissue (fresh weight) were observed, with no statistically significant differences in microbial cell density, richness, or diversity due to sprout type, sprout-growing facility, or seed lot. CLPP analyses revealed that the microbial communities associated with alfalfa and clover sprouts are more similar than those associated with the other sprout types tested. Variability among sprout types was more extensive than any differences between microbial communities associated with alfalfa and clover sprouts from different sprout-growing facilities and seed lots. These results indicate that the subsequent testing of biocontrol agents should focus on similar organisms for alfalfa and clover, but alternative types may be most suitable for the other sprout types tested. The inoculation of alfalfa sprouts with communities derived from various sprout types had a significant, source-independent effect on microbial community structure, indicating that the process of inoculation alters the dynamics of community development regardless of the types of organisms involved.
NASA Center KSC↗
PMA-PhyloChip DNA Microarray to Elucidate Viable Microbial Community Structure
Since the Viking missions in the mid-1970s, traditional culture-based methods have been used for microbial enumeration by various NASA programs. Viable microbes are of particular concern for spacecraft cleanliness, for forward contamination of extraterrestrial bodies (proliferation of microbes), and for crew health/safety (viable pathogenic microbes). However, a "true" estimation of viable microbial population and differentiation from their dead cells using the most sensitive molecular methods is a challenge, because of the stability of DNA from dead cells. The goal of this research is to evaluate a rapid and sensitive microbial detection concept that will selectively estimate viable microbes. Nucleic acid amplification approaches such as the polymerase chain reaction (PCR) have shown promise for reducing time to detection for a wide range of applications. The proposed method is based on the use of a fluorescent DNA intercalating agent, propidium monoazide (PMA), which can only penetrate the membrane of dead cells. The PMA-quenched reaction mixtures can be screened, where only the DNA from live cells will be available for subsequent PCR reaction and microarray detection, and be identified as part of the viable microbial community. An additional advantage of the proposed rapid method is that it will detect viable microbes and differentiate from dead cells in only a few hours, as opposed to less comprehensive culture-based assays, which take days to complete. This novel combination approach is called the PMA-Microarray method. DNA intercalating agents such as PMA have previously been used to selectively distinguish between viable and dead bacterial cells. Once in the cell, the dye intercalates with the DNA and, upon photolysis under visible light, produces stable DNA adducts. DNA cross-linked in this way is unavailable for PCR. Environmental samples suspected of containing a mixture of live and dead microbial cells/spores will be treated with PMA, and then incubated in the dark. Thereafter, the sample is exposed to visible light for five minutes, so that the DNA from dead cells will be cross-linked. Following this PMA treatment step, the sample is concentrated by centrifugation and washed (to remove excessive PMA) before DNA is extracted. The 16S rRNA gene fragments will be amplified by PCR to screen the total microbial community using PhyloChip DNA microarray analysis. This approach will detect only the viable microbial community since the PMA intercalated DNA from dead cells would be unavailable for PCR amplification. The total detection time including PCR reaction for low biomass samples will be a few hours. Numerous markets may use this technology. The food industry uses spore detection to validate new alternative food processing technologies, sterility, and quality. Pharmaceutical and medical equipment companies also detect spores as a marker for sterility. This system can be used for validating sterilization processes, water treatment systems, and in various public health and homeland security applications.
Venkateswaran, Kasthuri J.↗
Anaerobic decomposition of cellulose by allcaliphilic microbial Community of Owens Lake, California
The study of communities of microbial extremophiles from anaerobic sediments of Owens Lake and Mono Lake in California has established the presence of active microbial cellulolytic processes in both lakes. The prior study of the microbial diversity in Mono Lake showed that the trophic chain of organic decomposition includes secondary anaerobes that were found to be previously unknown species (Spirochaeta americana, Tindallia californiensis, and Desulfonatronum thiodismutans). And as we published earlier, the secondary anaerobes of Owens Lakes were morphologically very similar to those of Mono Lake. However, continuing comparison of the physiology and genetics has led to the conclusion that some links of organic decomposition in the trophic chain of Owens Lake are represented by different unknown species. A new isolate of a sugarlytic spirochete from Owens Lake, which was morphologically very similar to S. americana isolated from Mono Lake, was found to have different metabolic capacity such as the lack of capability to produce hydrogen during glucose fermentation. Furthermore, from the same bacterial community (from Owens Lake) another sugarlytic spore-forming alkaliphile (strain SCA) was isolated in pure culture. Here we discuss the geology and chemistry of Owens Lake as a unique ecosystem of Astrobiological significance. This paper also presents some of the characteristics for the novel isolates and describes their participation in the process of cellulose degradation.
Pikuta, Elena V.↗
Environmental Regulation of Microbial Community Structure
Most naturally occurring microbes live in complex microbial communities consisting of thousands of phylotypes of microorganisms living in close proximity. Each of these draws nutrients from the environment and releases metabolic waste products, which may in turn serve as substrates for other microbial groups. Gross environmental changes, such as irradiance level, hydrodynamic flow regime, temperature or water chemistry can directly affect the productivity of some community members, which in turn will affect other dependent microbial populations and rate processes. As a first step towards the development of "standard" natural communities of microorganisms for a variety of potential NASA applications, we are measuring biogeochemical cycling in artificially structured communities of microorganisms, created using natural microbial mat communities as inoculum. The responses of these artificially assembled communities of microorganisms to controlled shifts in ecosystem incubation conditions is being determined. This research requires close linking of environmental monitoring, with community composition in a closed and controlled incubation setting. We are developing new incubation chamber designs to allow for this integrated approach to examine the interplay between environmental conditions, microbial community composition and biogeochemical processes.
Bebout, Leslie↗
The Effect of Dilution on the Structure of Microbial Communities
To determine how dilution of microbial communities affects the diversity of the diluted assemblage a series of numerical simulations were conducted that determined the theoretical change in diversity, richness, and evenness of the community with serial dilution. The results of the simulation suggested that the effects are non linear with a high degree of dependence on the initial evenness of the community being diluted. A series of incubation experiments using a range of dilutions of raw sewage as an inoculum into sterile sewage was used for comparison to the simulations. The diluted communities were maintained in batch fed reactors (three day retention time) for nine days. The communities were harvested and examined by conventional plating and by molecular analysis of the whole-community DNA using AFLP and T-RFLP. Additional, CLPP analysis was also applied. The effects on richness predicted by the numerical simulations were confirmed by the analyses used. The diluted communities fell into three groups, a low dilution, intermediate dilution, and high dilution group, which corresponded well with the groupings obtained for community richness in simulation. The grouping demonstrated the non-linear nature of dilution of whole communities. Furthermore, the results implied that the undiluted community consisted of a few dominant types accompanied by a number of rare (low abundance) types as is typical in unevenly distributed communities.
Mills, Aaron L.↗
Amino acids as a source of organic nitrogen in Antarctic endolithic microbial communities
In the Antarctic Dry Valleys, cryptoendolithic microbial communities occur within porous sandstone rocks. Current understanding of the mechanisms of physiological adaptation of these communities to the harsh Antarctic environment is limited, because traditional methods of studying microbial physiology are very difficult to apply to organisms with extremely low levels of metabolic activity. In order to fully understand carbon and nitrogen cycling and nutrient uptake in cryptoendolithic communities, and the metabolic costs that the organisms incur in order to survive, it is necessary to employ molecular geochemical techniques such as amino acid analysis in addition to physiological methods.
Antarctica↗
Multi-scale variation in spatial heterogeneity for microbial community structure in an eastern Virginia agricultural field
To better understand the distribution of soil microbial communities at multiple spatial scales, a survey was conducted to examine the spatial organization of community structure in a wheat field in eastern Virginia (USA). Nearly 200 soil samples were collected at a variety of separation distances ranging from 2.5 cm to 11 m. Whole-community DNA was extracted from each sample, and community structure was compared using amplified fragment length polymorphism (AFLP) DNA fingerprinting. Relative similarity was calculated between each pair of samples and compared using geostatistical variogram analysis to study autocorrelation as a function of separation distance. Spatial autocorrelation was found at scales ranging from 30 cm to more than 6 m, depending on the sampling extent considered. In some locations, up to four different correlation length scales were detected. The presence of nested scales of variability suggests that the environmental factors regulating the development of the communities in this soil may operate at different scales. Kriging was used to generate maps of the spatial organization of communities across the plot, and the results demonstrated that bacterial distributions can be highly structured, even within a habitat that appears relatively homogeneous at the plot and field scale. Different subsets of the microbial community were distributed differently across the plot, and this is thought to be due to the variable response of individual populations to spatial heterogeneity associated with soil properties. c2003 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.
NASA Discipline Life Support Systems↗
Utilization of Alternate Chirality Enantiomers in Microbial Communities
Our previous study of chirality led to interesting findings for some anaerobic extremophiles: the ability to metabolize substrates with alternate chirality enantiomers of amino acids and sugars. We have subsequently found that not just separate microbial species or strains but entire microbial communities have this ability. The functional division within a microbial community on proteo- and sugarlytic links was also reflected in a microbial diet with L-sugars and D-amino acids. Several questions are addressed in this paper. Why and when was this feature developed in a microbial world? Was it a secondary de novo adaptation in a bacterial world? Or is this a piece of genetic information that has been left in modern genomes as an atavism? Is it limited exclusively to prokaryotes, or does this ability also occur in eukaryotes? In this article, we have used a broader approach to study this phenomenon using anaerobic extremophilic strains from our laboratory collection. A series of experiments were performed on physiologically different groups of extremophilic anaerobes (pure and enrichment cultures). The following characteristics were studied: 1) the ability to grow on alternate chirality enantiomers -- L-sugars and D- amino acids; 2) Growth-inhibitory effect of alternate chirality enantiomers; 3) Stickland reaction with alternate chirality amino acids. The results of this research are presented in this paper.
Pikuta, Elena V.↗
Sources of Hydrogen as Food for Deep Microbial Communities
To survive in deep subsurface environments autolithotrophic microbial communities require a sustainable food supply. One possible source is H2 which forms when H2O reacts with ferrous iron at rock surfaces or mineral grain boundaries to produce H2 plus ferric iron. The amount of H2 that can be supplied in this way, however, is relatively small and may not last for more than a few hundred or thousand years. A much larger reservoir of H2 exists in the rocks, inside mineral grains, arising from an as yet little-known redox conversion that affects OH- in nominally anhydrous minerals. These OH- represent small amounts of "water" that become incorporated during crystallization in H2O-laden environments. A corollary of the H2 formation from OH- is the formation of peroxy, an oxidized form of oxygen. While the peroxy become part of the mineral structure, the H2 molecules are diffusively mobile and can escape from within the mineral grains, entering the intergranular space. Assuming cautiously realistic number densities of OH- undergoing the in situ redox conversion to H2 plus peroxy, a 10 km deep rock column is expected to contain enough H2 to allow for a constant degassing rate of 50-100 nmole H2 per day per sq cm over 30 million years.
Freund, Friedemann↗
Hydrogen in rocks: an energy source for deep microbial communities
To survive in deep subsurface environments, lithotrophic microbial communities require a sustainable energy source such as hydrogen. Though H2 can be produced when water reacts with fresh mineral surfaces and oxidizes ferrous iron, this reaction is unreliable since it depends upon the exposure of fresh rock surfaces via the episodic opening of cracks and fissures. A more reliable and potentially more voluminous H2 source exists in nominally anhydrous minerals of igneous and metamorphic rocks. Our experimental results indicate that H2 molecules can be derived from small amounts of H2O dissolved in minerals in the form of hydroxyl, OH- or O3Si-OH, whenever such minerals crystallized in an H2O-laden environment. Two types of experiments were conducted. Single crystal fracture experiments indicated that hydroxyl pairs undergo an in situ redox conversion to H2 molecules plus peroxy links, O3Si/OO\SiO3. While the peroxy links become part of the mineral structure, the H2 molecules diffused out of the freshly fractured mineral surfaces. If such a mechanism occurred in natural settings, the entire rock column would become a volume source of H2. Crushing experiments to facilitate the outdiffusion of H2 were conducted with common crustal igneous rocks such as granite, andesite, and labradorite. At least 70 nmol of H2/g diffused out of coarsely crushed andesite, equivalent at standard pressure and temperature to 5,000 cm3 of H2/m3 of rock. In the water-saturated, biologically relevant upper portion of the rock column, the diffusion of H2 out of the minerals will be buffered by H2 saturation of the intergranular water film.
Hydrogen/analysis↗
Composition of Hydrothermal Vent Microbial Communities as Revealed by Analyses of Signature Lipids, Stable Carbon Isotopes and Aquificales Cultures
Extremely thermophilic microbial communities associated with the siliceous vent walls and outflow channel of Octopus Spring, Yellowstone National Park, have been examined for lipid biomarkers and carbon isotopic signatures. These data were compared with that obtained from representatives of three Aquificales genera. Thermocrinis ruber. "Thermocrinis sp. HI", Hydrogenobacter thermophilus TK-6, Aquifex pyrophilus and Aquifex aeolicus all contained phospholipids composed not only of the usual ester-linked fatty acids, but also ether-linked alkyls. The fatty acids of all cultured organisms were dominated by a very distinct pattern of n-C-20:1 and cy-C-21 compounds. The alkyl glycerol ethers were present primarily as CIS() monoethers with the expection of the Aquifex spp. in which dialkyl glycerol ethers with a boarder carbon-number distribution were also present. These Aquificales biomarker lipids were the major constituents in the lipid extracts of the Octopus Spring microbial samples. Two natural samples, a microbial biofilm growing in association with deposition of amorphous silica on the vent walls at 92 C, and the well-known 'pink-streamers community' (PSC), siliceous filaments of a microbial consortia growing in the upper outflow channel at 87 C were analyzed. Both the biofilm and PSC samples contained mono and dialkyl glycerol ethers with a prevalence of C-18 and C-20 alkyls. Phospholipid fatty acids were comprised of both the characteristic Aquificales n-C-20:1 and cy-C-21, and in addition, a series of iso-branched fatty acids from i-C-15:0 to i-C-21:0, With i-C-17:0 dominant in the PSC and i-C-19:0 in the biofilm, suggesting the presence of two major bacterial groups. Bacteriohopanepolyols were absent and the minute quantities of archaeol detected showed that Archaea were only minor constituents. Carbon isotopic compositions of the PSC yielded information about community structure and likely physiology. Biomass was C-13-depleted (10.9%) relative to available CO2 from the source water inorganic carbon pool with lipids further depleted by 6.3% relative to biomass The C-20-21 Aquificales fatty acids of the PSC were somewhat heavier than the iso-branched fatty acids. The carbon isotopic signatures of lipid biomarkers were also explored using a pure culture, T ruber, previously isolated from the PSC. Cells grown on C02 with O2 and both H2 and thiosulfate as electron donors were only slightly depleted (3.3%) relative to the C-source while cells grown on formate with O2 showed a major discrimination (19.7%), possibly the result of a metabolic branch point involving the assimilation of C-formate to biomass and the dissimilation to CO2 associated with energy production. T. ruber lipids were slightly heavier than biomass (+1.3%) whether cells were grown using CO2 or formate. Fatty acids from CO2 grown T. ruber cells were a so slightly heavier (average +2.1%) than biomass. The relatively depleted PSC C-20-21 fatty acids suggest that any associated Thermocrinis biomass would also be similarly depleted and much too light to be explained by growth on CO2. The C-fractionations determined with the pure culture suggest that growth of Thermocrinis in the PSC is more likely to occur on formate, presumably generated by geothermal activity. This study points to the value of the analysis of the structural and isotopic composition of lipid blomarkers both in pure culture studies, and in establishing community structure and physiology, as a complement to genomic profiles of microbial diversity. This is especially so when the members of the microbial community are novel and difficult to cultivate in the laboratory.
Jahnke, Linda L.↗
Culturability as an indicator of succession in microbial communities
Successional theory predicts that opportunistic species with high investment of energy in reproduction and wide niche width will be replaced by equilibrium species with relatively higher investment of energy in maintenance and narrower niche width as communities develop. Since the ability to rapidly grow into a detectable colony on nonselective agar medium could be considered as characteristic of opportunistic types of bacteria, the percentage of culturable cells may be an indicator of successional state in microbial communities. The ratios of culturable cells (colony forming units on R2A agar) to total cells (acridine orange direct microscopic counts) and culturable cells to active cells (reduction of 5-cyano-2,3-ditolyl tetrazolium chloride) were measured over time in two types of laboratory microcosms (the rhizosphere of hydroponically grown wheat and aerobic, continuously stirred tank reactors containing plant biomass) to determine the effectiveness of culturabilty as an index of successional state. The culturable cell:total cell ratio in the rhizosphere decreased from approximately 0.25 to less than 0.05 during the first 30-50 days of plant growth, and from 0.65 to 0.14 during the first 7 days of operation of the bioreactor. The culturable cell:active cell ratio followed similar trends, but the values were consistently greater than the culturable cell:total cell ratio, and even exceeded I in early samples. Follow-up studies used a cultivation-independent method, terminal restriction fragment length polymorphisms (TRFLP) from whole community DNA, to assess community structure. The number of TRFLP peaks increased with time, while the number of culturable types did not, indicating that the general decrease in culturability is associated with a shift in community structure. The ratio of respired to assimilated C-14-labeled amino acids increased with the age of rhizosphere communities, supporting the hypothesis that a shift in resource allocation from growth to maintenance occurs with time. Results from this work indicate that the percentage of culturable cells may be a useful method for assessing the successional state of microbial communities.
NASA Center KSC↗
Microbial community structure at the U.S.-Joint Global Ocean Flux Study Station ALOHA: Inverse methods for estimating biochemical indicator ratios
Modeling biogeochemical fluxes in the marine plankton requires the application of factors for extrapolation of biomass indicators measured in the field (chlorophyll a, adenosine triphosphate, bacterial counts) to biomass carbon or nitrogen. These are often inferred from culture studies and are poorly constrained for natural populations. At least squares inverse method with a simple linear model constrains the values of several common indicator ratios, giving self-consistent solutions that provide useful information about the structure of the microbial community at our North Pacific Ocean study site (Station ALOHA (A Long-term Oligotrophic Habitat Assessment)). These results indicate that the fraction of the microbial biomass that is autotrophic (pigmented) is greater in the mixed layer than at the deep chlorophyll maximum layer and that heterotrophic bacteria are a significant but not necessarily predominant component of the microbial community in the euphotic zone.
Christian, James R.↗
Microbial astronauts: assembling microbial communities for advanced life support systems
Extension of human habitation into space requires that humans carry with them many of the microorganisms with which they coexist on Earth. The ubiquity of microorganisms in close association with all living things and biogeochemical processes on Earth predicates that they must also play a critical role in maintaining the viability of human life in space. Even though bacterial populations exist as locally adapted ecotypes, the abundance of individuals in microbial species is so large that dispersal is unlikely to be limited by geographical barriers on Earth (i.e., for most environments "everything is everywhere" given enough time). This will not be true for microbial communities in space where local species richness will be relatively low because of sterilization protocols prior to launch and physical barriers between Earth and spacecraft after launch. Although community diversity will be sufficient to sustain ecosystem function at the onset, richness and evenness may decline over time such that biological systems either lose functional potential (e.g., bioreactors may fail to reduce BOD or nitrogen load) or become susceptible to invasion by human-associated microorganisms (pathogens) over time. Research at the John F. Kennedy Space Center has evaluated fundamental properties of microbial diversity and community assembly in prototype bioregenerative systems for NASA Advanced Life Support. Successional trends related to increased niche specialization, including an apparent increase in the proportion of nonculturable types of organisms, have been consistently observed. In addition, the stability of the microbial communities, as defined by their resistance to invasion by human-associated microorganisms, has been correlated to their diversity. Overall, these results reflect the significant challenges ahead for the assembly of stable, functional communities using gnotobiotic approaches, and the need to better define the basic biological principles that define ecosystem processes in the space environment. Copyright 2004 Springer-Verlag.
Review↗