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BIOMEX (BIOlogy and Mars EXperiment) is an ESA/Roscosmos space exposure experiment housed within the exposure facility EXPOSE-R2 outside the Zvezda module on the International Space Station (ISS). The design of the multiuser facility supports-among others-the BIOMEX investigations into the stability and level of degradation of space-exposed biosignatures such as pigments, secondary metabolites, and cell surfaces in contact with a terrestrial and Mars analog mineral environment. In parallel, analysis on the viability of the investigated organisms has provided relevant data for evaluation of the habitability of Mars, for the limits of life, and for the likelihood of an interplanetary transfer of life (theory of lithopanspermia). In this project, lichens, archaea, bacteria, cyanobacteria, snow/permafrost algae, meristematic black fungi, and bryophytes from alpine and polar habitats were embedded, grown, and cultured on a mixture of martian and lunar regolith analogs or other terrestrial minerals. The organisms and regolith analogs and terrestrial mineral mixtures were then exposed to space and to simulated Mars-like conditions by way of the EXPOSE-R2 facility. In this special issue, we present the first set of data obtained in reference to our investigation into the habitability of Mars and limits of life. This project was initiated and implemented by the BIOMEX group, an international and interdisciplinary consortium of 30 institutes in 12 countries on 3 continents. Preflight tests for sample selection, results from ground-based simulation experiments, and the space experiments themselves are presented and include a complete overview of the scientific processes required for this space experiment and postflight analysis. The presented BIOMEX concept could be scaled up to future exposure experiments on the Moon and will serve as a pretest in low Earth orbit.
Landslides
(2022)
Erosion by landslides is a common phenomenon in mountain regions around the globe, affecting all climatic zones. Landslides facilitate bedrock weathering, pedogenesis and ecological succession, being key drivers of biodiversity. Landslide chronosequences have long been used for studies of vegetation succession in initial ecosystems, but they further offer ideal model systems for studies of soil development and microbial community succession. In this review we synthesize the state of knowledge on the role of landslides in ecosystems, their influence on element cycles and interactions with biota. Further, we discuss feedback mechanisms between global warming, landslide activity and greenhouse gas emissions. In the view of increasing anthropogenic influence and climate change, soils are becoming a critical resource. Due to their ubiquity, landslide chronosequences have the potential to provide critical insights into soil development under different climates and thereby contribute to future soil restoration efforts.
Draft Genome Sequence of Nocardioides alcanivorans NGK65(T), a Hexadecane-Degrading Bacterium
(2022)
The Gram-positive bacterium Nocardioides alcanivorans NGK65(T) was isolated from plastic-polluted soil and cultivated on medium with polyethylene as the single carbon source. Nanopore sequencing revealed the presence of candidate enzymes for the biodegradation of polyethylene. Here, we report the draft genome of this newly described member of the terrestrial plastisphere.
Tropical Lake Sentani in the Indonesian Province Papua consists of four separate basins and is surrounded by a catchment with a very diverse geology. We characterized the surface sediment (upper 5 cm) of the lake's four sub-basins based on multivariate statistical analyses (principal component analysis, hierarchical clustering) of major element compositions obtained by X-ray fluorescence scanning. Three types of sediment are identified based on distinct compositional differences between rivers, shallow/proximal and deep/distal lake sediments. The different sediment types are mainly characterized by the correlation of elements associated with redox processes (S, Mn, Fe), carbonates (Ca), and detrital input (Ti, Al, Si, K) derived by river discharge. The relatively coarse-grained river sediments mainly derive form the mafic catchment geology and contribution of the limestone catchment geology is only limited. Correlation of redox sensitive and detrital elements are used to reveal oxidation conditions, and indicate oxic conditions in river samples and reducing conditions for lake sediments. Organic carbon (TOC) generally correlates with redox sensitive elements, although a correlation between TOC and individual elements change strongly between the three sediment types. Pyrite is the quantitatively dominant reduced sulfur mineral, monosulfides only reach appreciable concentrations in samples from rivers draining mafic and ultramafic catchments. Our study shows large spatial heterogeneity within the lake's sub-basins that is mainly caused by catchment geology and topography, river runoff as well as the bathymetry and the depth of the oxycline. We show that knowledge about lateral heterogeneity is crucial for understanding the geochemical and sedimentological variations recorded by these sediments. The highly variable conditions make Lake Sentani a natural laboratory, with its different sub-basins representing different depositional environments under identical tropical climate conditions.
Dryland xeric conditions exert a deterministic effect on microbial communities, forcing life into refuge niches. Deposited rocks can form a lithic niche for microorganisms in desert regions. Mineral weathering is a key process in soil formation and the importance of microbial-driven mineral weathering for nutrient extraction is increasingly accepted. Advances in geobiology provide insight into the interactions between microorganisms and minerals that play an important role in weathering processes. In this study, we present the examination of the microbial diversity in dryland rocks from the Tsauchab River banks in Namibia. We paired culture-independent 16S rRNA gene amplicon sequencing with culture-dependent (isolation of bacteria) techniques to assess the community structure and diversity patterns. Bacteria isolated from dryland rocks are typical of xeric environments and are described as being involved in rock weathering processes. For the first time, we extracted extra- and intracellular DNA from rocks to enhance our understanding of potentially rock-weathering microorganisms. We compared the microbial community structure in different rock types (limestone, quartz-rich sandstone and quartz-rich shale) with adjacent soils below the rocks. Our results indicate differences in the living lithic and sublithic microbial communities.
James Ross Island (JRI) offers the exceptional opportunity to study microbial-driven pedogenesis without the influence of vascular plants or faunal activities (e.g., penguin rookeries). In this study, two soil profiles from JRI (one at Santa Martha Cove - SMC, and another at Brandy Bay BB) were investigated, in order to gain information about the initial state of soil formation and its interplay with prokaryotic activity, by combining pedological, geochemical and microbiological methods. The soil profiles are similar with respect to topographic position and parent material but are spatially separated by an orographic barrier and therefore represent windward and leeward locations towards the mainly southwesterly winds. These different positions result in differences in electric conductivity of the soils caused by additional input of bases by sea spray at the windward site and opposing trends in the depth functions of soil pH and electric conductivity. Both soils are classified as Cryosols, dominated by bacterial taxa such as Actinobacteria, Proteobacteria, Acidobacteria, Gemmatimonadetes and Chloroflexi. A shift in the dominant taxa was observed below 20 cm in both soils as well as an increased abundance of multiple operational taxonomic units (OTUs) related to potential chemolithoautotrophic Acidiferrobacteraceae. This shift is coupled by a change in microstructure. While single/pellicular grain microstructure (SMC) and platy microstructure (BB) are dominant above 20 cm, lenticular microstructure is dominant below 20 cm in both soils. The change in microstructure is caused by frequent freeze-thaw cycles and a relative high water content, and it goes along with a development of the pore spacing and is accompanied by a change in nutrient content. Multivariate statistics revealed the influence of soil parameters such as chloride, sulfate, calcium and organic carbon contents, grain size distribution and pedogenic oxide ratios on the overall microbial community structure and explained 49.9% of its variation. The correlation of the pedogenic oxide ratios with the compositional distribution of microorganisms as well as the relative abundance certain microorganisms such as potentially chemolithotrophic Acidiferrobacteraceae-related OTUs could hint at an interplay between soil-forming processes and microorganisms.
Microbial community composition and abundance after millennia of submarine permafrost warming
(2019)
Warming of the Arctic led to an increase in permafrost temperatures by about 0.3 degrees C during the last decade. Permafrost warming is associated with increasing sediment water content, permeability, and diffusivity and could in the long term alter microbial community composition and abundance even before permafrost thaws. We studied the long-term effect (up to 2500 years) of submarine permafrost warming on microbial communities along an onshore-offshore transect on the Siberian Arctic Shelf displaying a natural temperature gradient of more than 10 degrees C. We analysed the in situ development of bacterial abundance and community composition through total cell counts (TCCs), quantitative PCR of bacterial gene abundance, and amplicon sequencing and correlated the microbial community data with temperature, pore water chemistry, and sediment physicochemical parameters. On timescales of centuries, permafrost warming coincided with an overall decreasing microbial abundance, whereas millennia after warming microbial abundance was similar to cold onshore permafrost. In addition, the dissolved organic carbon content of all cores was lowest in submarine permafrost after millennial-scale warming. Based on correlation analysis, TCC, unlike bacterial gene abundance, showed a significant rank-based negative correlation with increasing temperature, while bacterial gene copy numbers showed a strong negative correlation with salinity. Bacterial community composition correlated only weakly with temperature but strongly with the pore water stable isotopes delta O-18 and delta D, as well as with depth. The bacterial community showed substantial spatial variation and an overall dominance of Actinobacteria, Chloroflexi, Firmicutes, Gemmatimonadetes, and Proteobacteria, which are amongst the microbial taxa that were also found to be active in other frozen permafrost environments. We suggest that, millennia after permafrost warming by over 10 degrees C, microbial community composition and abundance show some indications for proliferation but mainly reflect the sedimentation history and paleoenvironment and not a direct effect through warming.
Since the beginning of the Anthropocene, lacustrine biodiversity has been influenced by climate change and human activities. These factors advance the spread of harmful cyanobacteria in lakes around the world, which affects water quality and impairs the aquatic food chain. In this study, we assessed changes in cyanobacterial community dynamics via sedimentary DNA (sedaDNA) from well-dated lake sediments of Lake Tiefer See, which is part of the Klocksin Lake Chain spanning the last 350 years. Our diversity and community analysis revealed that cyanobacterial communities form clusters according to the presence or absence of varves. Based on distance-based redundancy and variation partitioning analyses (dbRDA and VPA) we identified that intensified lake circulation inferred from vegetation openness reconstructions, delta C-13 data (a proxy for varve preservation) and total nitrogen content were abiotic factors that significantly explained the variation in the reconstructed cyanobacterial community from Lake Tiefer See sediments. Operational taxonomic units (OTUs) assigned to Microcystis sp. and Aphanizomenon sp. were identified as potential eutrophication-driven taxa of growing importance since circa common era (ca. CE) 1920 till present. This result is corroborated by a cyanobacteria lipid biomarker analysis. Furthermore, we suggest that stronger lake circulation as indicated by non-varved sediments favoured the deposition of the non-photosynthetic cyanobacteria sister clade Sericytochromatia, whereas lake bottom anoxia as indicated by subrecent- and recent varves favoured the Melainabacteria in sediments. Our findings highlight the potential of high-resolution amplicon sequencing in investigating the dynamics of past cyanobacterial communities in lake sediments and show that lake circulation, anoxic conditions, and human-induced eutrophication are main factors explaining variations in the cyanobacteria community in Lake Tiefer See during the last 350 years.
Soil bacteria play a fundamental role in pedogenesis. However, knowledge about both the impact of climate and slope aspects on microbial communities and the consequences of these items in pedogenesis is lacking. Therefore, soil-bacterial communities from four sites and two different aspects along the climate gradient of the Chilean Coastal Cordillera were investigated. Using a combination of microbiological and physicochemical methods, soils that developed in arid, semi-arid, mediterranean, and humid climates were analyzed. Proteobacteria, Acidobacteria, Chloroflexi, Verrucomicrobia, and Planctomycetes were found to increase in abundance from arid to humid climates, while Actinobacteria and Gemmatimonadetes decreased along the transect. Bacterial-community structure varied with climate and aspect and was influenced by pH, bulk density, plant-available phosphorus, clay, and total organic-matter content. Higher bacterial specialization was found in arid and humid climates and on the south-facing slope and was likely promoted by stable microclimatic conditions. The presence of specialists was associated with ecosystem-functional traits, which shifted from pioneers that accumulated organic matter in arid climates to organic decomposers in humid climates. These findings provide new perspectives on how climate and slope aspects influence the composition and functional capabilities of bacteria, with most of these capabilities being involved in pedogenetic processes.
Lake Towuti is a tectonic basin, surrounded by ultramafic rocks. Lateritic soils form through weathering and deliver abundant iron (oxy)hydroxides but very little sulfate to the lake and its sediment. To characterize the sediment biogeochemistry, we collected cores at three sites with increasing water depth and decreasing bottom water oxygen concentrations. Microbial cell densities were highest at the shallow site a feature we attribute to the availability of labile organic matter (OM) and the higher abundance of electron acceptors due to oxic bottom water conditions. At the two other sites, OM degradation and reduction processes below the oxycline led to partial electron acceptor depletion. Genetic information preserved in the sediment as extracellular DNA (eDNA) provided information on aerobic and anaerobic heterotrophs related to Nitrospirae. Chloroflexi, and Therrnoplasmatales. These taxa apparently played a significant role in the degradation of sinking OM. However, eDNA concentrations rapidly decreased with core depth. Despite very low sulfate concentrations, sulfate-reducing bacteria were present and viable in sediments at all three sites, as confirmed by measurement of potential sulfate reduction rates. Microbial community fingerprinting supported the presence of taxa related to Deltaproteobacteria and Firmicutes with demonstrated capacity for iron and sulfate reduction. Concomitantly, sequences of Ruminococcaceae, Clostridiales, and Methanornicrobiales indicated potential for fermentative hydrogen and methane production. Such first insights into ferruginous sediments showed that microbial populations perform successive metabolisms related to sulfur, iron, and methane. In theory, iron reduction could reoxidize reduced sulfur compounds and desorb OM from iron minerals to allow remineralization to methane. Overall, we found that biogeochemical processes in the sediments can be linked to redox differences in the bottom waters of the three sites, like oxidant concentrations and the supply of labile OM. At the scale of the lacustrine record, our geomicrobiological study should provide a means to link the extant subsurface biosphere to past environments.
Ferruginous (Fe-rich, SO4-poor) conditions are generally restricted to freshwater sediments on Earth today, but were likely widespread during the Archean and Proterozoic Eons. Lake Towuti, Indonesia, is a large ferruginous lake that likely hosts geochemical processes analogous to those that operated in the ferruginous Archean ocean. The metabolic potential of microbial communities and related biogeochemical cycling under such conditions remain largely unknown. We combined geochemical measurements (pore water chemistry, sulfate reduction rates) with metagenomics to link metabolic potential with geochemical processes in the upper 50 cm of sediment. Microbial diversity and quantities of genes for dissimilatory sulfate reduction (dsrAB) and methanogenesis (mcrA) decrease with increasing depth, as do rates of potential sulfate reduction. The presence of taxa affiliated with known iron- and sulfate-reducers implies potential use of ferric iron and sulfate as electron acceptors. Pore-water concentrations of acetate imply active production through fermentation. Fermentation likely provides substrates for respiration with iron and sulfate as electron donors and for methanogens that were detected throughout the core. The presence of ANME-1 16S and mcrA genes suggests potential for anaerobic methane oxidation. Overall our data suggest that microbial community metabolism in anoxic ferruginous sediments support coupled Fe, S and C biogeochemical cycling.
Permafrost-affected soils are among the most obvious ecosystems in which current microbial controls on organic matter decomposition are changing as a result of global warming. Warmer conditions in polygonal tundra will lead to a deepening of the seasonal active layer, provoking changes in microbial processes and possibly resulting in exacerbated carbon degradation under increasing anoxic conditions. To identify current microbial assemblages in carbon rich, water saturated permafrost environments, four polygonal tundra sites were investigated on Herschel Island and the Yukon Coast, Western Canadian Arctic. Ion Torrent sequencing of bacterial and archaeal 16S rRNA amplicons revealed the presence of all major microbial soil groups and indicated a local, vertical heterogeneity of the polygonal tundra soil community with increasing depth. Microbial diversity was found to be highest in the surface layers, decreasing towards the permafrost table. Quantitative PCR analysis of functional genes involved in carbon and nitrogen-cycling revealed a high functional potential in the surface layers, decreasing with increasing active layer depth. We observed that soil properties driving microbial diversity and functional potential varied in each study site. These results highlight the small-scale heterogeneity of geomorphologically comparable sites, greatly restricting generalizations about the fate of permafrost-affected environments in a warming Arctic.
The Arctic ecosystem, a reservoir of genetic microbial diversity, represents a virtually unlimited source of microorganisms that could interact with human beings. Despite continuous exploration of Arctic habitats and description of their microbial communities, bacterial phenotypes commonly associated with pathogenicity, such as hemolytic activity, have rarely been reported. In this study, samples of snow, fresh and marine water, soil, and sediment from several habitats in the Arctic archipelago of Svalbard were collected during Summer, 2017. Bacterial isolates were obtained after incubation on oligotrophic media at different temperatures and their hemolytic potential was assessed on sheep blood agar plates. Partial (alpha) or true (beta) hemolysis was observed in 32 out of 78 bacterial species. Genes expressing cytolytic compounds, such as hemolysins, likely increase the general fitness of the producing microorganisms and confer a competitive advantage over the availability of nutrients in natural habitats. In environmental species, the nutrient-acquisition function of these compounds presumably precedes their function as toxins for mammalian erythrocytes. However, in the light of global warming, the presence of hemolytic bacteria in Arctic environments highlights the possible risks associated with these microorganisms in the event of habitat melting/destruction, ecosystem transition, and re-colonization.
Sulfate reduction is the quantitatively most important process to degrade organic matter in anoxic marine sediment and has been studied intensively in a variety of settings. Guaymas Basin, a young marginal ocean basin, offers the unique opportunity to study sulfate reduction in an environment characterized by organic-rich sediment, high sedimentation rates, and high geothermal gradients (100-958 degrees C km(-1)). We measured sulfate reduction rates (SRR) in samples taken during the International Ocean Discovery Program (IODP) Expedition 385 using incubation experiments with radiolabeled (SO42-)-S-35 carried out at in situ pressure and temperature. The highest SRR (387 nmol cm(-3) d(-1)) was recorded in near-surface sediments from Site U1548C, which had the steepest geothermal gradient (958 degrees C km(-1)). At this site, SRR were generally over an order of magnitude higher than at similar depths at other sites (e.g., 387-157 nmol cm(-3) d(-1) at 1.9 mbsf from Site U1548C vs. 46-1.0 nmol cm(-3) d(-1) at 2.1 mbsf from Site U1552B). Site U1546D is characterized by a sill intrusion, but it had already reached thermal equilibrium and SRR were in the same range as nearby Site U1545C, which is minimally affected by sills. The wide temperature range observed at each drill site suggests major shifts in microbial community composition with very different temperature optima but awaits confirmation by molecular biological analyses. At the transition between the mesophilic and thermophilic range around 40 degrees C-60 degrees C, sulfate-reducing activity appears to be decreased, particularly in more oligotrophic settings, but shows a slight recovery at higher temperatures.
The Cheb Basin (CZ) is a shallow Neogene intracontinental basin filled with fluvial and lacustrine sediments that is located in the western part of the Eger Rift. The basin is situated in a seismically active area and is characterized by diffuse degassing of mantle-derived CO2 in mofette fields. The Hartousov mofette field shows a daily CO2 flux of 23-97 tons of CO2 released over an area of 0.35 km(2) and a soil gas concentration of up to 100% CO2. The present study aims to explore the geo-bio interactions provoked by the influence of elevated CO2 concentrations on the geochemistry and microbial community of soils and sediments. To sample the strata, two 3-m cores were recovered. One core stems from the center of the degassing structure, whereas the other core was taken 8 m from the ENE and served as an undisturbed reference site. The sites were compared regarding their geochemical features, microbial abundances, and microbial community structures. The mofette site is characterized by a low pH and high TOC/sulfate contents. Striking differences in the microbial community highlight the substantial impact of elevated CO2 concentrations and their associated side effects on microbial processes. The abundance of microbes did not show a typical decrease with depth, indicating that the uprising CO2-rich fluid provides sufficient substrate for chemolithoautotrophic anaerobic microorganisms. Illumine MiSeq sequencing of the 16S rRNA genes and multivariate statistics reveals that the pH strongly influences microbial composition and explains around 38.7% of the variance at the mofette site and 22.4% of the variance between the mofette site and the undisturbed reference site. Accordingly, acidophilic microorganisms (e.g., OTUs assigned to Acidobacteriaceae and Acidithiobacillus) displayed a much higher relative abundance at the mofette site than at the reference site. The microbial community at the mofette site is characterized by a high relative abundance of methanogens and taxa involved in sulfur cycling. The present study provides intriguing insights into microbial life and geo-bio interactions in an active seismic region dominated by emanating mantle-derived CO2-rich fluids, and thereby builds the basis for further studies, e.g., focusing on the functional repertoire of the communities. However, it remains open if the observed patterns can be generalized for different time-points or sites.
More than 41% of the Earth’s land area is covered by permanent or seasonally arid dryland ecosystems. Global development and human activity have led to an increase in aridity, resulting in ecosystem degradation and desertification around the world. The objective of the present work was to investigate and compare the microbial community structure and geochemical characteristics of two geographically distinct saline pan sediments in the Kalahari Desert of southern Africa. Our data suggest that these microbial communities have been shaped by geochemical drivers, including water content, salinity, and the supply of organic matter. Using Illumina 16S rRNA gene sequencing, this study provides new insights into the diversity of bacteria and archaea in semi-arid, saline, and low-carbon environments. Many of the observed taxa are halophilic and adapted to water-limiting conditions. The analysis reveals a high relative abundance of halophilic archaea (primarily Halobacteria), and the bacterial diversity is marked by an abundance of Gemmatimonadetes and spore-forming Firmicutes. In the deeper, anoxic layers, candidate division MSBL1, and acetogenic bacteria (Acetothermia) are abundant. Together, the taxonomic information and geochemical data suggest that acetogenesis could be a prevalent form of metabolism in the deep layers of a saline pan.
On Earth, chemolithoautothrophic and anaerobic microorganisms such as methanogenic archaea are regarded as model organisms for possible subsurface life on Mars. For this reason, the methanogenic strain Methanosarcina soligelidi (formerly called Methanosarcina spec. SMA-21), isolated from permafrost-affected soil in northeast Siberia, has been tested under Martian thermo-physical conditions. In previous studies under simulated Martian conditions, high survival rates of these microorganisms were observed. In our study we present a method to measure methane production as a first attempt to study metabolic activity of methanogenic archaea during simulated conditions approaching conditions of Mars-like environments. To determine methanogenic activity, a measurement technique which is capable to measure the produced methane concentration with high precision and with high temporal resolution is needed. Although there are several methods to detect methane, only a few fulfill all the needed requirements to work within simulated extraterrestrial environments. We have chosen laser spectroscopy, which is a non-destructive technique that measures the methane concentration without sample taking and also can be run continuously. In our simulation, we detected methane production at temperatures down to -5 degrees C, which would be found on Mars either temporarily in the shallow subsurface or continually in the deep subsurface. The pressure of 50 kPa which we used in our experiments, corresponds to the expected pressure in the Martian near subsurface. Our new device proved to be fully functional and the results indicate that the possible existence of methanogenic archaea in Martian subsurface habitats cannot be ruled out. (C) 2013 Published by Elsevier Ltd.
The Low Earth Orbit (LEO) experiment Biology and Mars Experiment (BIOMEX) is an interdisciplinary and international space research project selected by ESA. The experiment will be accommodated on the space exposure facility EXPOSE-R2 on the International Space Station (ISS) and is foreseen to be launched in 2013. The prime objective of BIOMEX is to measure to what extent biomolecules, such as pigments and cellular components, are resistant to and able to maintain their stability under space and Mars-like conditions. The results of BIOMEX will be relevant for space proven biosignature definition and for building a biosignature data base (e.g. the proposed creation of an international Raman library). The library will be highly relevant for future space missions such as the search for life on Mars. The secondary scientific objective is to analyze to what extent terrestrial extremophiles are able to survive in space and to determine which interactions between biological samples and selected minerals (including terrestrial, Moon- and Mars analogs) can be observed under space and Mars-like conditions. In this context, the Moon will be an additional platform for performing similar experiments with negligible magnetic shielding and higher solar and galactic irradiation compared to LEO. Using the Moon as an additional astrobiological exposure platform to complement ongoing astrobiological LEO investigations could thus enhance the chances of detecting organic traces of life on Mars. We present a lunar lander mission with two related objectives: a lunar lander equipped with Raman and PanCam instruments which can analyze the lunar surface and survey an astrobiological exposure platform. This dual use of testing mission technology together with geo- and astrobiological analyses will significantly increase the science return, and support the human preparation objectives. It will provide knowledge about the Moon's surface itself and, in addition, monitor the stability of life-markers, such as cells, cell components and pigments, in an extraterrestrial environment with much closer radiation properties to the surface of Mars. The combination of a Raman data base of these data together with data from LEO and space simulation experiments, will lead to further progress on the analysis and interpretation of data that we will obtain from future Moon and Mars exploration missions.