Microbial ecology of permafrost, due to its ecological and astrobiological importance, has been in the focus of studies in past decades. Although permafrost is an ancient and stable environment, it is also subjected to current climate changes. Permafrost degradation often results in generation of thaw ponds, a phenomenon not only reported mainly from polar regions but also present in high-altitude permafrost environments. Our knowledge about microbial communities of thaw ponds in these unique, remote mountain habitats is sparse. This study presents the first culture collection and results of the next-generation DNA sequencing (NGS) analysis of bacterial communities inhabiting a high-altitude permafrost thaw pond. In February 2016, a permafrost thaw pond on the Ojos del Salado at 5900 m a.s.l. (meters above sea level) was sampled as part of the Hungarian Dry Andes Research Programme. A culture collection of 125 isolates was established, containing altogether 11 genera belonging to phyla Bacteroidetes, Actinobacteria, and Proteobacteria. Simplified bacterial communities with a high proportion of candidate and hitherto uncultured bacteria were revealed by Illumina MiSeq NGS. Water of the thaw pond was dominated by Bacteroidetes and Proteobacteria, while in the sediment of the lake and permafrost, members of Acidobacteria, Actinobacteria, Bacteroidetes, Patescibacteria, Proteobacteria, and Verrucomicrobia were abundant. This permafrost habitat can be interesting as a potential Mars analog.

Terrestrial mud volcanoes usually develop in overpressured, hydrocarbon-bearing sedimentary basins where argillaceous, viscous fluids and gases find passages to the surface. In this study mud samples collected at the Beciu mud volcano area (Romania) were examined using 16S rRNA gene amplicon sequencing technique. Bacterial communities were dominated by Proteobacteria, Patescibaceria, Bacteriodota, and Campilobacterota while Archaea by Halobacterota and Nanoarchaeota. All the most abundant taxa can be connected to the characteristic methane production of the onshore mud volcanism and/or the presence of a deep subsurface salt layer. The discharged methane might be utilized by the detected ubiquitous anaerobic methane oxidizers (ANME-1, ANME-2a-2b, ANME-3) coupling the reaction with the sulfate or sulfur reduction by representatives of genera Sulfurovum, Sulfurimonas, Desulfobacterales, Desulfuromonadales, Halanaeroarchaeum, and Halodesulfurarchaeum. In addition to methanotrophs, methylotrophic and acetoclastic methanogens were also detected. Most of the identified OTUs were associated with halophilic taxa. The results suggest that prokaryotes inhabiting the mud volcanoes can be participated in the closely interconnected methane and sulfur cycles.

High-altitude saline lakes (located more than 3000 m a.s.l.) provide multiple environmental extremities for polyextremophilic bacteria. In this study, lake sediment samples from Laguna Santa Rosa and microbial mat samples from the warm water pool of Laguna Verde (Puna de Atacama, Chile) were examined by cultivation and pyrosequencing. The 16S rRNA gene-based identification showed that most of the bacterial isolates belonged to different moderately halophilic Marinobacter species (Proteobacteria). Sample-specific occurrence was characteristic of genera Caenispirillum, Halomonas, Idiomarina, Nitratireductor and Salinarimonas (Proteobacteria), Planococcus, Jeotgalibacillus and Paraliobacillus (Firmicutes), Psychroflexus (Bacteroidetes) and Arthrobacter (Actinobacteria). Using cultivation-independent technique, the benthic communities of both lakes were dominated by sequences related to the phyla Proteobacteria and Bacteroidetes. In addition, representatives of phyla Actinobacteria, Chlorobi, Chloroflexi, Cloacimonetes, Cyanobacteria, Deferribacteres, Deinococcus-Thermus, Firmicutes, Gracilibacteria, Latescibacteria, Lentisphaerae, Parcubacteria, Planctomycetes, Spirochaetae, Tenericutes and Verrucomicrobia were present at least 1% relative abundance. Large differences were explored in the bacterial community composition of the sediment and mat samples at the level of the identified families. It is hypothesized that depending on the type of benthic habitat, different bacteria – involved in the phototrophy based primary production as well as the mainly anaerobic biodegradation of organic materials – can participate in the local carbon, nitrogen, and sulfur cycles.

Soil bacterial communities play a remarkable role in nutrient cycling, significantly affecting soil organic material content, soil fertility, and, in an indirect way, plant succession processes. Conversely, vegetation type influences microbial soil life. The present study compared the bacterial microbiome composition, diversity and catabolic activity profile of topsoil samples collected under three different forest types (a twice-coppiced black locust stand, a young, naturally reforested, and a middle-aged mixed pedunculate oak stand) planted on former arable land in the early 20th century. Diversity indices determined during 16S ribosomal RNA sequencing-based metagenome analysis indicated that the black locust stand had the highest soil bacterial community diversity. At the phylum level, Acidobacteriota, Actinobacteriota, Proteobacteria, Verrucomicrobiota, Bacteroidota, and Gemmatimonadota were the most abundant taxa in the forest soils. Concerning soil parameters, redundancy analysis revealed that pH had the highest impact on bacterial community structure and pH, and soil organic carbon content on the samples’ respiration patterns. As for catabolic activity, the recently clearcut oak forest showed the lowest substrate-induced respiration, and citrate was the main driver for the inter-stand variability of microbial activity. Our results confirm that soil parameters and forest type influence the composition and functioning of the soil bacterial microbiome.

Changes resulting from different tillage practices can affect the structure of microbial communities, thereby altering soil ecosystems and their functioning. The aim of this study was to explore and compare the physical, chemical properties and bacterial community composition of soils from different land use types (forest, grassland, vineyard, and arable field) in a small catchment. 16S rRNA gene-based amplicon sequencing was used to reveal the taxonomic diversity of summer and autumn soil samples taken from two different slope positions. The greater the anthropogenic impact was on the type of land use, the greater the change was in soil physical and chemical parameters. All sample types were dominated by the phyla Pseudomonadota, Acidobacteriota, Actinobacteriota, Bacteroidota and Verrucomicrobiota. Differences in the relative abundance of various bacterial taxa reflected the different land use types, the seasonality, and the topography. These diversity changes were consistent with the differences in soil properties. Graphical abstract

Nowadays, one of the most important challenges is to ensure sustainable agricultural management of crops such as maize (Zea mays L.). Long-term crop production, however, may influence the soil properties, the composition and activity of microbial communities. The aim of this study was to compare the catabolic activity and taxonomic diversity of bacterial communities inhabiting the soil of a non-fertilized maize monoculture and a natural grassland. Samples were taken from the horizons A and C in the first part of the vegetation period. MicroResp™ technique was used to explore the catabolic potential of microbial communities and next generation amplicon sequencing to reveal the bacterial diversity. Based on the catabolic activity results, higher differences were revealed among the soil horizons than the different land uses. The highest degree carbon source utilization was detected in the soil horizon A of the natural grassland. The taxonomic composition of bacterial communities was dominated by Proteobacteria. The relative abundance of other dominant phyla (Acidobacteria, Bacteroidetes, Verrucomicrobia, Actinobacteria, Planctomycetes, Gemmatimonadetes, Chloroflexi and Patescibacteria) varied according to both the land use and soil depth. Amplicon sequences belonging to genera of r-strategist “copiotrophic” and K-strategist “oligotrophic” bacteria were identified from the soils of both maize monoculture and grassland.