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Antarctica is the last pristine environment on Earth, its biota being adapted to the harsh and extreme polar climate. Until now, soil formation and vegetation development in continental Antarctica were considered very slow due to the extreme conditions of this polar desert. Since the austral summer 2002/2003, a long-term monitoring network of the terrestrial ecosystems (soils, vegetation, active layer thickness) has been established at Victoria Land (VL) across a > 500 km latitudinal gradient of coastal sites (73 degrees -77 degrees S). In only one decade large ecosystem changes were detected. Climate was characterized by a significant increase of thawing degree days in northern VL and of autumn air temperature. No extreme climatic events (such as hot spells) where detected in the study period. Soil chemistry suffered large quantitative changes, clearly indicating rapid pedogenetic processes. In most soils the upper layers exhibited a strong alkalinization (pH increases up to 3 units) and increases in conductivity, anions and cations (in particular of SO4 and Na). The largest changes were observed in soils with low vegetation cover. Statistically significant differences in soil chemistry were detected between soils with high and low vegetation cover, the former showing lower pH, conductivity, Na and Cl. Most plots exhibited changes of total cover, species richness and floristic composition, with vegetation expansion in soils with low vegetation cover and the largest increase recorded at Apostrophe Island (northern VL). Principal Component Analysis (PCA) identified the main trend of vegetation change, with a shift from lower to higher cover and a secondary trend of change associated with a gradient of water availability, consistent with an increase in water instead of snow. Redundancy analysis (RDA) identified the trend of change in soil chemistry with increases in pH, conductivity, anions and cations associated with the concomitant decrease in C, N, NO3, PO4. The RDA confirmed that soil changes were associated with a gradient of vegetation change (from low to high cover) as well as of water availability, as already indirectly outlined by the PCA. Field manipulation experiments carried out at five locations of the network between 73 degrees S and 77 degrees S, simulating increases of precipitation from snow or water additions didn't induce changes in soil pH, indicating that pulse events of snow accumulation or melting could not trigger persistent soil pH changes. These data allow hypothesize the occurrence of a main ecosystem change occurring at regional scale at Victoria Land. The slight air warming and its consequences on soil chemistry and vegetation, further highlight the sensitivity of the fragile Antarctic ecosystems to the consequences of even small changes in climate.
Strain NGK35T is a motile, Gram-stain-negative, rod-shaped (1.0-2.1 mu m long and 0.6-0.8 mu m wide), aerobic bacterium that was isolated from plastic-polluted landfill soil. The strain grew at temperatures between 6 and 37 degrees C (optimum, 28 degrees C), in 0-10 % NaCl (optimum, 1 %) and at pH 6.0-9.5 (optimum, pH 7.5-8.5).
It was positive for cytochrome c oxidase, catalase as well as H2S production, and hydrolysed casein and urea. It used a variety of different carbon sources including citrate, lactate and pyruvate.
The predominant membrane fatty acids were C-16:1 cis9 and C-16:0, followed by C-17:0 cyclo and C-18:1 cis11. The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine, followed by diphosphatidyglycerol. The only quinone was ubiquinone Q-8. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NGK35(T) belongs to the genus Paenalcaligenes (family Alcaligenaceae), appearing most closely related to Paenalcaligenes hominis CCUG 53761A(T) (96.90 %) and Paenalcaligenes suwonensis ABC02-12(T) (96.94 %).
The genomic DNA G+C content of strain NGK35(T) was 52.1 mol%. Genome-based calculations (genome-to-genome distance, average nucleotide identity and DNA G+C content) clearly indicated that the isolate represents a novel species within the genus Paenalcaligenes.
Based on phenotypic and molecular characterization, strain NGK35(T) can clearly be differentiated from its phylogenetic neighbours establishing a novel species, for which the name Paenalcaligenes niemegkensis sp. nov. is proposed.
The type strain is NGK35T (=DSM 113270(T)=NCCB 100854(T)).
A circular, single-contig Methanobacterium sp. metagenome-assembled genome (MAG) was recovered from high-CO2 enrichments inoculated with drill core material from the tectonic Eger Rift terrestrial subsurface.
Annotation of the recovered MAG highlighted putative methanogenesis genes, providing valuable information on archaeal activity in the deep biosphere.
The Gram-negative bacterium Paenalcaligenes niemegkensis NGK35(T) was isolated from plastic debris in an abandoned landfill.
It has the ability to grow on polyethylene and hexadecane as the sole carbon sources. Here, we report the corresponding draft genome, which contains 3.66 Mbp and is characterized by a G+C content of 52.1%.
A metagenome-assembled genome (MAG), named Methanosarcina sp. strain ERenArc_MAG2, was obtained from a 3-month-old H-2/CO2 atmosphere enrichment culture, originally inoculated with 60-m deep drill core sediment collected from the tectonic Eger Rift terrestrial subsurface.
Annotation of the recovered draft genome revealed putative archaeal methanogenesis genes in the deep biosphere.
A metagenome-assembled genome (MAG), named Methanosarcina sp. strain ERenArc_MAG2, was obtained from a 3-month-old H-2/CO2 atmosphere enrichment culture, originally inoculated with 60-m deep drill core sediment collected from the tectonic Eger Rift terrestrial subsurface.
Annotation of the recovered draft genome revealed putative archaeal methanogenesis genes in the deep biosphere.
Sedimentary ancient DNA-based studies have been used to probe centuries of climate and environmental changes and how they affected cyanobacterial assemblages in temperate lakes. Due to cyanobacteria containing potential bloom-forming and toxin-producing taxa, their approximate reconstruction from sediments is crucial, especially in lakes lacking long-term monitoring data. To extend the resolution of sediment record interpretation, we used high-throughput sequencing, amplicon sequence variant (ASV) analysis, and quantitative PCR to compare pelagic cyanobacterial composition to that in sediment traps (collected monthly) and surface sediments in Lake Tiefer See. Cyanobacterial composition, species richness, and evenness was not significantly different among the pelagic depths, sediment traps and surface sediments (p > 0.05), indicating that the cyanobacteria in the sediments reflected the cyanobacterial assemblage in the water column. However, total cyanobacterial abundances (qPCR) decreased from the metalimnion down the water column. The aggregate-forming (Aphanizomenon) and colony-forming taxa (Snowella) showed pronounced sedimentation. In contrast, Planktothrix was only very poorly represented in sediment traps (meta- and hypolimnion) and surface sediments, despite its highest relative abundance at the thermocline (10 m water depth) during periods of lake stratification (May-October). We conclude that this skewed representation in taxonomic abundances reflects taphonomic processes, which should be considered in future DNA-based paleolimnological investigations.
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.
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.
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.
Cyanobacteria are important primary producers in temperate freshwater ecosystems. However, studies on the seasonal and spatial distribution of cyanobacteria in deep lakes based on high-throughput DNA sequencing are still rare. In this study, we combined monthly water sampling and monitoring in 2019, amplicon sequence variants analysis (ASVs; a proxy for different species) and quantitative PCR targeting overall cyanobacteria abundance to describe the seasonal and spatial dynamics of cyanobacteria in the deep hard-water oligo-mesotrophic Lake Tiefer See, NE Germany. We observed significant seasonal variation in the cyanobacterial community composition (p < 0.05) in the epi- and metalimnion layers, but not in the hypolimnion. In winter-when the water column is mixed-picocyanobacteria (Synechococcus and Cyanobium) were dominant. With the onset of stratification in late spring, we observed potential niche specialization and coexistence among the cyanobacteria taxa driven mainly by light and nutrient dynamics. Specifically, ASVs assigned to picocyanobacteria and the genus Planktothrix were the main contributors to the formation of deep chlorophyll maxima along a light gradient. While Synechococcus and different Cyanobium ASVs were abundant in the epilimnion up to the base of the euphotic zone from spring to fall, Planktothrix mainly occurred in the metalimnetic layer below the euphotic zone where also overall cyanobacteria abundance was highest in summer. Our data revealed two potentially psychrotolerant (cold-adapted) Cyanobium species that appear to cope well under conditions of lower hypolimnetic water temperature and light as well as increasing sediment-released phosphate in the deeper waters in summer. The potential cold-adapted Cyanobium species were also dominant throughout the water column in fall and winter. Furthermore, Snowella and Microcystis-related ASVs were abundant in the water column during the onset of fall turnover. Altogether, these findings suggest previously unascertained and considerable spatiotemporal changes in the community of cyanobacteria on the species level especially within the genus Cyanobium in deep hard-water temperate lakes.
Nocardioides alcanivorans sp. nov., a novel hexadecane-degrading species isolated from plastic waste
(2022)
Strain NGK65(T), a novel hexadecane degrading, non-motile, Gram-positive, rod-to-coccus shaped, aerobic bacterium, was isolated from plastic polluted soil sampled at a landfill.
Strain NGK65(T) hydrolysed casein, gelatin, urea and was catalase-positive. It optimally grew at 28 degrees C. in 0-1% NaCl and at pH 7.5-8.0. Glycerol, D-glucose, arbutin, aesculin, salicin, potassium 5-ketogluconate. sucrose, acetate, pyruvate and hexadecane were used as sole carbon sources.
The predominant membrane fatty acids were iso-C-16:0 followed by iso-C(17:)0 and C-18:1 omega 9c. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and hydroxyphosphatidylinositol.
The cell-wall peptidoglycan type was A3 gamma, with LL-diaminopimelic acid and glycine as the diagnostic amino acids. MK 8 (H-4) was the predominant menaquinone. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NGK65(T) belongs to the genus Nocardioides (phylum Actinobacteria). appearing most closely related to Nocardioides daejeonensis MJ31(T) (98.6%) and Nocardioides dubius KSL-104(T) (98.3%).
The genomic DNA G+C content of strain NGK65(T) was 68.2%.
Strain NGK65(T) and the type strains of species involved in the analysis had average nucleotide identity values of 78.3-71.9% as well as digital DNA-DNA hybridization values between 22.5 and 19.7%, which clearly indicated that the isolate represents a novel species within the genus Nocardioides.
Based on phenotypic and molecular characterization, strain NGK65(T) can clearly be differentiated from its phylogenetic neighbours to establish a novel species, for which the name Nocardioides alcanivorans sp. nov. is proposed.
The type strain is NGK65(T) (=DSM 113112(T)=NCCB 100846(T)).
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.
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.
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.
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.
The Hartousov mofette system is a natural CO2 degassing site in the central Cheb Basin (Eger Rift, Central Europe). In early 2016 a 108 m deep core was obtained from this system to investigate the impact of ascending mantle-derived CO2 on indigenous deep microbial communities and their surrounding life habitat. During drilling, a CO2 blow out occurred at a depth of 78.5 meter below surface (mbs) suggesting a CO2 reservoir associated with a deep low-permeable CO2-saturated saline aquifer at the transition from Early Miocene terrestrial to lacustrine sediments. Past microbial communities were investigated by hopanoids and glycerol dialkyl glycerol tetraethers (GDGTs) reflecting the environmental conditions during the time of deposition rather than showing a signal of the current deep biosphere. The composition and distribution of the deep microbial community potentially stimulated by the upward migration of CO2 starting during Mid Pleistocene time was investigated by intact polar lipids (IPLs), quantitative polymerase chain reaction (qPCR), and deoxyribonucleic acid (DNA) analysis. The deep biosphere is characterized by microorganisms that are linked to the distribution and migration of the ascending CO2-saturated groundwater and the availability of organic matter instead of being linked to single lithological units of the investigated rock profile. Our findings revealed high relative abundances of common soil and water bacteria, in particular the facultative, anaerobic and potential iron-oxidizing Acidovorax and other members of the family Comamonadaceae across the whole recovered core. The results also highlighted the frequent detection of the putative sulfate-oxidizing and CO2-fixating genus Sulfuricurvum at certain depths. A set of new IPLs are suggested to be indicative for microorganisms associated to CO2 accumulation in the mofette system.
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.
Due to a lack of well-preserved terrestrial climate archives, paleoclimate studies are sparse in southwestern Africa. Because there are no perennial lacustrine systems in this region, this study relies on a saline pan as an archive for climate information in the western Kalahari (Namibia). Molecular biological and biogeochemical analyses were combined to examine the response of indigenous microbial communities to modern and past climate-induced environmental conditions. The 16S rRNA gene high-throughput sequencing was applied to sediment samples from Omongwa pan to characterize the modern microbial diversity. Highest diversity of microorganisms, dominated by the extreme halophilic archaeon Halobacteria and by the bacterial phylum Gemmatimonadetes, was detected in the near-surface sediments of Omongwa pan. In deeper sections abundance and diversity significantly decreases and Bacillus, known to form spores, become dominant. Lipid biomarkers for living and past microbial life were analyzed to track the influence of climate variation on the abundance of microbial communities from the Last Glacial Maximum to Holocene time. Since water is an inevitable requirement for microbial life, in this dry region the abundance of past microbial biomarkers was evaluated to conclude on periods of increased paleoprecipitation in the past. The data point to a period of increased humidity in the western Kalahari during the Last Glacial to Holocene transition indicating a southward shift of the Intertropical Convergence Zone during this period. Comparison with results from a southwestern Kalahari pan suggests complex displacements of the regional atmospheric systems since the Last Glacial Maximum.
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.