Quantifying biodiversity and asymptotics for a sequence of random strings

We study the set of incompressible strings for various resource bounded versions of Kolmogorov complexity. The resource bounded versions of Kolmogorov complexity we study are polynomial time CD complexity defined by Sipser, the nondeterministic variant CND due to Buhrman and Fortnow, and the polynomial space bounded Kolmogorov complexity CS introduced by Hartmanis. For all of these measures we define the set of random strings $\mathrm{R}^{\mathit{CD}}_t$, $\mathrm{R}^{\mathit{CND}}_t$, and $\mathrm{R}^{\mathit{CS}}_t$ as the set of strings x such that $\mathit{CD}^t(x)$, $\mathit{CND}^t(x)$, and $\mathit{CS}^s(x)$ is greater than or equal to the length of x for s and t polynomials. We show the following: $\mathrm{MA} \subseteq \mathrm{NP}^{\mathrm{R}^{\mathit{CD}}_t}$, where $\mathrm{MA}$ is the class of Merlin--Arthur games defined by Babai. $\mathrm{AM} \subseteq \mathrm{NP}^{\mathrm{R}^{\mathit{CND}}_t}$, where $\mathrm{AM}$ is the class of Arthur--Merlin games. $\mathrm{PSPACE} \subseteq \mathrm{NP}^{\mathrm{cR}^{\mathit{CS}}_s}$. In the last item $\mathrm{cR}^{\mathit{CS}}_s$ is the set of pairs $\langle x,y \rangle$ so that x is random given y. These results show that the set of random strings for various resource bounds is hard for complexity classes under nondeterministic reductions. This paper contrasts the earlier work of Buhrman and Mayordomo where they show that for polynomial time deterministic reductions the set of exponential time Kolmogorov random strings is not complete for EXP.

Chapter 14 - Microbial Ecology in Extreme Acidic Environments: Use of Molecular Tools

Microbial functional diversity in the phyllosphere and laimosphere of different desert plants

Extreme environments on Earth host a large diversity of microbial life. Bacteria, archaea, and fungi are able to survive under one or several extreme conditions including extreme ranges of temperature, pressure, pH or salinity. Despite extensive research on extremophilic microorganisms, a relatively unexplored frontier within the study of the deep biosphere is the survey of the diversity of microorganisms inhabiting deep geothermal reservoirs used for energy production. These sites offer unique access to investigate life in the deep biosphere. The conditions in these reservoirs are often within the range of the known limits of life, which makes them a suitable habitat for various extremophilic microorganisms. Moreover, microbial-driven processes such as microbially induced scaling or corrosion can decrease the efficacy of geothermal power plant systems. The present review summarizes the current knowledge and uncertainties surrounding microbial life in deep geothermal reservoirs. As the knowledge in deep geothermal fluids is still scarce, the microbial diversity in analogous environments, such as surface geothermal springs, deep-sea hydrothermal vents or deep subsurface environments, is also summarized here. The high diversity of microorganisms inhabiting these analogous environments suggests that deep geothermal fluids may host an unsuspected microbial diversity. Moreover, the challenges associated to the study of microorganisms in geothermal fluids are reviewed. These include notably challenges linked to sampling, DNA extraction from low biomass samples, DNA amplification and sequencing of unknown communities, and biases induced by comparison of the sequences obtained to reference databases. Such biases are even stronger concerning fungi and archaea, as specific databases are less extensive than those for bacteria. A broader knowledge on microorganisms in deep geothermal fluids may not only allow to reduce the negative impact of microbial activity in geothermal power plants, but could also provide new insights into the evolution of microorganisms and their survival in extreme environments.

Bio-mining microorganisms are a key factor affecting the metal recovery rate of bio-leaching, which inevitably produces an extremely acidic environment. As a powerful tool for exploring the adaptive mechanisms of microorganisms in extreme environments, omics technologies can greatly aid our understanding of bio-mining microorganisms and their communities on the gene, mRNA, and protein levels. These omics technologies have their own advantages in exploring microbial diversity, adaptive evolution, changes in metabolic characteristics, and resistance mechanisms of single strains or their communities to extreme environments. These technologies can also be used to discover potential new genes, enzymes, metabolites, metabolic pathways, and species. In addition, integrated multi-omics analysis can link information at different biomolecular levels, thereby obtaining more accurate and complete global adaptation mechanisms of bio-mining microorganisms. This review introduces the current status and future trends in the application of omics technologies in the study of bio-mining microorganisms and their communities in extreme environments.

The immune system is a crucial part of the body's defense against infection and disease. However, individuals in antigen-limited environments face unique challenges that can weaken their immune systems. This systematic review aimed to investigate the impact of an exposure to an isolated, confined and extreme (ICE) environment with limited antigen diversity on human immune parameters. A systematic literature search was conducted using PubMed, Web of Science and Cochrane Library to identify relevant studies on immune system parameters in ICE environments. The studies were grouped by ICE type (space missions, microgravity simulations like bed rest studies, space simulation units like MARS500, and Antarctic research stations) to allow for clearer comparison and analysis of immune outcomes. Analysis of 140 studies revealed considerable heterogeneity in study designs and outcomes, reflecting the complexity of immune responses across ICE environments. Nevertheless, immune dysregulation was consistently observed across environments. Space missions and Antarctic stations, in particular, showed pronounced immune changes, likely due to low antigen diversity and extreme conditions, with higher rates of infections and allergic responses suggesting increased vulnerability. Space simulation units exhibited immune changes similar to those in actual space missions, while gravity simulation studies, which focus on fluid shifts and bone loss, showed fewer immune alterations. Across environments, most immunological measures returned to baseline after isolation, indicating resilience and the potential for recovery upon re-exposure to diverse antigens. Reduced antigen diversity in ICE environments disrupts immune function, with effects often compounded by extreme conditions. Although immune resilience and recovery post-isolation are promising, the heterogeneity in current studies highlights the need for targeted research to identify specific immune vulnerabilities and to develop countermeasures. Such measures could reduce immune-related health risks for individuals in isolated settings, including astronauts, polar researchers, and vulnerable populations on Earth, such as the elderly or immunocompromised, thereby enhancing resilience in confined environments. https://www.crd.york.ac.uk/prospero/, identifier CRD42023476132.

Microbial communication, particularly that of quorum sensing, plays an important role in regulating gene expression in a range of organisms. Although this phenomenon has been well studied in relation to, for example, virulence gene regulation, the focus of this article is to review our understanding of the role of microbial communication in extreme environments. Cell signaling regulates many important microbial processes and may play a pivotal role in driving microbial functional diversity and ultimately ecosystem function in extreme environments. Several recent studies have characterized cell signaling in modern analogs to early Earth communities (microbial mats), and characterization of cell signaling systems in these communities may provide unique insights in understanding the microbial interactions involved in function and survival in extreme environments. Cell signaling is a fundamental process that may have co-evolved with communities and environmental conditions on the early Earth. Without cell signaling, evolutionary pressures may have even resulted in the extinction rather than evolution of certain microbial groups. One of the biggest challenges in extremophile biology is understanding how and why some microbial functional groups are located where logically they would not be expected to survive, and tightly regulated communication may be key. Finally, quorum sensing has been recently identified for the first time in archaea, and thus communication at multiple levels (potentially even inter-domain) may be fundamental in extreme environments.

Environmental parameters, and not phylogeny, determine the composition of extracellular polymeric substances in microbial mats from extreme environments

Puna wetlands and salars are a unique extreme environment all over the world, since their locations are in high-altitude saline deserts, largely influenced by volcanic activity. Ultraviolet radiation, arsenic content, high salinity, and low dissolved oxygen content, together with extreme daily temperature fluctuations and oligotrophic conditions, shape an environment that recreates the early Earth and, even more so, extraterrestrial conditions. Microbes inhabiting extreme environments face these conditions with different strategies, including formation of intricate microbial communities with an increasing degree of complexity. In that way, biofilms, mats, endoevaporitic mats, domes, and microbialites have been found to exist in association with salars, lagoons, and even volcanic fumaroles in Central Andean extreme environments. They form microbial ecosystems, where light and O2 availability decrease with depth stratification, promoting functional group diversity. This microbial diversity, together with the geochemistry, may favor the precipitation of minerals. This chapter summarizes general concepts in the environmental microbiology of extreme Andean ecosystems, which are explored throughout this book.

Chapter 7 - Biodiversity of deep ocean on development of biofilms: Biofouling communities and corrosion performance of materials

Microbes from extreme environments do not necessarily require extreme culture conditions. Perhaps the most extreme environments known, deep-sea hydrothermal vent sites, support an incredible array of archaea, bacteria, and fungi, many of which have now been cultured. Microbes cultured from extreme environments have not disappointed in the natural products arena; diverse bioactive secondary metabolites have been isolated from cultured extreme-tolerant microbes, extremophiles, and deep-sea microbes. The contribution of vent microbes to our arsenal of natural products will likely grow, given the culturability of vent microbes; their metabolic, physiologic, and phylogenetic diversity; numerous reports of bioactive natural products from microbes inhabiting high acid, high temperature, or high pressure environments; and the recent isolation of new chroman derivatives and siderophores from deep-sea hydrothermal vent bacteria.

High-fluoride hot springs serve as a natural laboratory for investigating microbial adaptation and variations in community structure under extreme environments. This study utilized water chemistry analysis and 16S rRNA gene sequencing to investigate the correlation between high-fluoride hot springs and microbial community structure and diversity. The results show that the five hot springs exhibited an average F− content of 15.04 mg/L, with weakly alkaline pH, high total dissolved solids, and Na+ as the dominant cation. The hydrochemical type was classified as HCO3⋅SO4-Na, consistent with the chemical characteristics of high-fluorine water. Microbial abundance and diversity were significantly reduced in the hot springs as compared to the surface water and groundwater samples. The dominant phyla in the study area included Pseudomonadota, Cyanobacteriota, Bacteroidota, and Actinomycetota. The genus-level composition varied significantly across samples, with no dominant genus observed universally. The specific genera present in different samples exhibit unique functional attributes, such as Tepidimonas, Rhodobacter, Hyphomonas, Parvibaculum, Polynucleobacter and Limnohabitans. Cluster analysis confirmed that dissimilarity coefficients highlight the significant influence of microbial abundance on inter-sample differences among hot springs. Redundancy analysis of the top 11 phyla by abundance in water samples revealed that the presence of F− exerts inhibitory effects on microbial growth.

The Arctic Ocean supports a unique and dynamic microbial community, yet its composition, structure, and response to environmental shifts remain incompletely understood. In this study, 16S rRNA gene metabarcoding (targeting the V3-V4 and V4-V5 hypervariable regions) was used to assess surface water microbial diversity across 20 stations in the Barents Sea, focusing on latitudinal variations within two contrasting current systems: the West Spitsbergen Current (WSC) and the East Spitsbergen Current (ESC). Our results showed that the microbial community is dominated by three primary families—Pseudoalteromonadaceae, Moraxellaceae, and Flavobacteriaceae (14.20%). Comparative analysis of the V3-V4 and V4-V5 regions reveals that each region captures different aspects of microbial diversity, with V4-V5 detecting a higher number of unique families. Analysis through Nonmetric Multidimensional Scaling (NMDS) reveals distinct community separations between the WSC and ESC, though ANOSIM results indicate no significant within-system differences. Environmental parameters, including pH and temperature, appear closely linked with community composition, reflecting the influence of climatic and oceanographic processes on microbial structure. As global climate change continues to reshape Arctic environments, monitoring microbial diversity is essential to understand and predict shifts in the Arctic Ocean`s ecosystem functions.

Microorganisms living in polar regions rely on specialized mechanisms to adapt to extreme environments. The study of their stress adaptation mechanisms is a hot topic in international microbiology research. In this study, a bacterial strain (Arc9.136) isolated from Arctic marine sediments was selected to implement polyphasic taxonomic identification based on factors such as genetic characteristics, physiological and biochemical properties, and chemical composition. The results showed that strain Arc9.136 is classified to the genus Nocardioides, for which the name Nocardioides arcticus sp. nov. is proposed. The ozone hole over the Arctic leads to increased ultraviolet (UV-B) radiation, and low temperatures lead to increased dissolved content in seawater. These extreme environmental conditions result in oxidative stress, inducing a strong response in microorganisms. Based on the functional classification of significantly differentially expressed genes under 1 mM H2O2 stress, we suspect that Arc9.136 may respond to oxidative stress through the following strategies: (1) efficient utilization of various carbon sources to improve carbohydrate transport and metabolism; (2) altering ion transport and metabolism by decreasing the uptake of divalent iron (to avoid the Fenton reaction) and increasing the utilization of trivalent iron (to maintain intracellular iron homeostasis); (3) increasing the level of cell replication, DNA repair, and defense functions, repairing DNA damage caused by H2O2; (4) and changing the composition of lipids in the cell membrane and reducing the sensitivity of lipid peroxidation. This study provides insights into the stress resistance mechanisms of microorganisms in extreme environments and highlights the potential for developing low-temperature active microbial resources.

Microbial diversity of hypersaline environments: a metagenomic approach