The Atacama Desert in Northern Chile as an Analog Model of Mars

The Atacama Desert is by far the driest and oldest desert on Earth, showing a unique combination of environmental extremes (extreme dryness, the highest UV radiation levels on Earth, and highly saline and oxidizing soils), explaining why the Atacama has been largely investigated as a Mars analog model for almost 20 years. Based on the source and the amount of water available for life and its analogy with Mars, two ecosystems are of interest in the Atacama: its Coastal Range and the much drier hyperarid core, which we here review in detail. Members of the three domains of life have been found across these ecosystems living at the limit of habitability, suggesting the potential dry limits for each domain and also unveiling the highly patchy distribution of microbial life in its most extreme regions. The thorough study of the Atacama has allowed us to understand how life has adapted to its extreme conditions, the specific habitats that life occupies in each case (thus suggesting the most likely places in which to search for evidence for life on Mars), and the number of biosignatures detected across this desert. Also, the characterization of west-to-east transects across this desert has shown to be of significant value to understand the potential adaptations that Martian microorganisms may have followed in an ever-drying planet. All of this explains why the Atacama is actively used as the testing ground of the technologies (detection instruments, rovers, etc.) that were sent and will be sent to Mars. We also highlight the need to better inform the exact locations of the sites studied to understand general trends, the need to identify the true native microbial species of the Atacama, and the impact of climate change on the most arid and most Martian desert of Earth.

Re-Thinking the Roles of Pathogens and Mutualists: Exploring the Continuum of Symbiosis in the Context of Microbial Ecology and Evolution

Systems of classification are important for guiding research activities and providing a common platform for discussion and investigation. One such system is assigning microbial taxa to the roles of mutualists and pathogens. Yet, there are often challenges and even inconsistencies in reports of research findings when microbial taxa display behaviors outside of these two static conditions (e.g. commensal). Over the last two decades, there has been some effort to highlight a continuum of symbiosis, wherein certain microbial taxa may exhibit mutualistic or pathogenic traits depending on environmental contexts, life stages, and plant host associations. However, gaps remain in understanding how to apply the continuum approach to host-microbe pairs across a range of environmental and ecological factors. This commentary presents an alternative framework for evaluating the continuum of symbiosis using dominant archetypes that define symbiotic ranges. We focus particularly on fungi and bacteria, though we recognize that archaea and other microeukaryotes play important roles in host-microbe interactions that may be described by this approach. This framework is centered in eco-evolutionary theory and aims to enhance communication among researchers, as well as prioritize holistic consideration of the factors shaping microbial life strategies. We discuss the influence of plant-mediated factors, habitat constraints, co-evolutionary forces, and the genetic contributions which shape different microbial lifestyles. Looking to the future, using a continuum of symbiosis paradigm will enable greater flexibility in defining the roles of target microbes and facilitate a more holistic view of the complex and dynamic relationship between microbes and plants.

Genetic diversity in terrestrial subsurface ecosystems impacted by geological degassing

Earth’s mantle releases 38.7 ± 2.9 Tg/yr CO2 along with other reduced and oxidized gases to the atmosphere shaping microbial metabolism at volcanic sites across the globe, yet little is known about its impact on microbial life under non-thermal conditions. Here, we perform comparative metagenomics coupled to geochemical measurements of deep subsurface fluids from a cold-water geyser driven by mantle degassing. Key organisms belonging to uncultivated Candidatus Altiarchaeum show a global biogeographic pattern and site-specific adaptations shaped by gene loss and inter-kingdom horizontal gene transfer. Comparison of the geyser community to 16 other publicly available deep subsurface sites demonstrate a conservation of chemolithoautotrophic metabolism across sites. In silico replication measures suggest a linear relationship of bacterial replication with ecosystems depth with the exception of impacted sites, which show near surface characteristics. Our results suggest that subsurface ecosystems affected by geological degassing are hotspots for microbial life in the deep biosphere.

The colors of life: an interdisciplinary artist-in-residence project to research fungal pigments as a gateway to empathy and understanding of microbial life

Background Biological pigmentation is one of the most intriguing traits of many fungi. It holds significance to scientists, as a sign of biochemical metabolism and organism-environment interaction, and to artists, as the source of natural colors that capture the beauty of the microbial world. Furthermore, the functional roles and aesthetic appeal of biological pigmentation may be a path to inspiring human empathy for microorganisms, which is key to understanding and preserving microbial biodiversity. A project focused on cross-species empathy was initiated and conducted as part of an artist-in-residence program in 2021. The aim of this residency is to bridge the current divide between science and art through interdisciplinary practice focused on fungi. Results The residency resulted in multiple products that are designed for artistic and scientific audiences with the central theme of biological pigmentation in fungi and other microorganisms. The first product is a video artwork that focuses on Aspergillus niger as a model organism that produces melanin pigment in a biosynthetic process similar to that of humans. The growth and morphology of this commonplace organism are displayed through video, photo, animation, and time-lapse footage, inviting the viewer to examine the likenesses and overlaps between humans and fungi. The second product is The Living Color Database, an online compendium of biological colors for scientists, artists, and designers. It links organisms across the tree of life, focusing on fungi, bacteria, and archaea, and the colors they express through biological pigmentation. Each pigment is represented in terms of its chemistry, its related biosynthesis, and its color expressions according to different indices: HEX, RGB, and Pantone. It is available at color.bio. Conclusions As fungal biotechnology continues to mature into new application areas, it is as important as ever that there is human empathy for these organisms to promote the preservation and appreciation of fungal biodiversity. The products presented here provide paths for artists, scientists, and designers to understand microorganisms through the lens of color, promoting interspecies empathy through research, teaching, and practice.

Applications of Metagenomics for Unrevealing the Extended Horizons of Microbiota Prevalence from Soil to Human Health

Phylogenetic analysis of different ecosystems has shown that the number of microbial communities in a single sample exceeds their cultured counterparts. Microbes have been found throughout nature and can thrive in adverse conditions. Besides inhabiting diverse environments, they also play a key role in the maintenance of the ecosystem. Most of these microbes are either unculturable or difficult to culture with conventional culturing methods. Metagenomics is an emerging field of science that has been in the light for a decade and offers a potential way to assess microbial diversity. The development of metagenomics opens new ways to study genetic material directly from the environmental samples. DNA sequencing and synthesis technologies are making it possible to read and write entire genomes. The huge amount of data obtained from genome sequencing inevitably requires bioinformatics tools to handle and further process them for analysis. Advances in DNA sequencing and high-performance computing have brought about exemplar improvement in metagenomics, allowing in-depth study of the largely unexplored frontier of microbial life. This culture-independent method provides extensive information regarding the structure, composition, and function of the diverse assemblages of the environmental microbes. The current review presents an overview of the technical aspects of metagenomics along with its diverse applications.

Organic Oil Recovery - Resident Microbial Enhanced Production Pilot in Bahrain

Tatweer Petroleum has been involved in a Pilot study to determine the efficacy of Organic Oil Recovery (OOR), a unique form of microbial enhanced oil recovery as a means of maximising oil recovery from its Rubble reservoir within the Awali field. OOR harnesses microbial life already present in an oil-bearing reservoir to improve oil recovery through changes in interfacial tensions, which in the case of Rubble will increase the heavy oil's mobility and improve recovery rates and reservoir wettability. These changes could increase recoverable reserves and extend field life through improved oil recovery with negligible topsides modifications. The Pilot injection is implemented by injecting a specific nutrient blend directly at the wellhead with ordinary pumping equipment. The well is then shut-in for an incubation period and thereafter returned to production. In Tatweer Petroleum's Awali field the Rubble reservoir is one of the shallowest oil reservoirs in the Bahrain and the first oil discovery in the Gulf Cooperation Council (GCC) region. The reservoir can be found at depths of around 1400 – 1900 ft. During initial laboratory testing of the Rubble target wells the reservoir showed a diverse and abundant resident ecology which has been proven capable of undergoing the necessary characteristic changes to facilitate enhanced production from the target wells. The Pilot test on one of these wells, called Well (A) within this paper, took place in July 2020 and due to this process, the ecology of this well showed these same changes in characteristics in the reservoir along with an associated oil response. The full method of implementation of the Pilot test will also be discussed in detail and will include any challenges and/or successes in this area. The initial state ecology reports of Well (A) are demonstrated and compared to that of post-Pilot test ecology. We also present the production figures for the well prior to and post the Pilot implementation. A correlation will be demonstrated between changes in ecology and an increase in production.

Microbial Life on the Surface of Microplastics in Natural Waters

Major water-polluting microplastics (for example, polyethylene, polypropylene and others) have lower density than water. Therefore, they are concentrated in the neustonic layer near the water-air interface altogether with dissolved or colloidal natural organic matter, hydrophobic cells and spores of bacteria. This can cause environmental and public health problems because the floating micro- and nanoparticles of plastics could be coated with biofilm of hydrophobic and often putative pathogenic bacteria. Biofilm-coated microplastics are more attractive for consumption by aquatic animals than pure microplastics, and that increases the negative impacts of microplastics. So, impacts of even small quantities of microplastics in aquatic environments must be accounted for considering their accumulation in the micro-layer of water-air interphase and its interaction with bacterioneuston. Microorganisms attached to the surface of microplastic particles could interact with them, use them as substrates for growth, to change properties and biodegrade. The study of microbial life on the surface of microplastic particles is one of the key topics to understanding their role in the environment.

Microbial processes during deposition and diagenesis of Banded Iron Formations

Banded Iron Formations (BIFs) are marine chemical sediments consisting of alternating iron (Fe)-rich and silica (Si)-rich bands which were deposited throughout much of the Precambrian era. BIFs represent important proxies for the geochemical composition of Precambrian seawater and provide evidence for early microbial life. Iron present in BIFs was likely precipitated in the form of Fe3+ (Fe(III)) minerals, such as ferrihydrite (Fe(OH)3), either through the metabolic activity of anoxygenic photoautotrophic Fe2+ (Fe(II))-oxidizing bacteria (photoferrotrophs), by microaerophilic bacteria, or by the oxidation of dissolved Fe(II) by O2 produced by early cyanobacteria. However, in addition to oxidized Fe-bearing minerals such as hematite (FeIII2O3), (partially) reduced minerals such as magnetite (FeIIFeIII2O4) and siderite (FeIICO3) are found in BIFs as well. The presence of reduced Fe in BIFs has been suggested to reflect the reduction of primary Fe(III) minerals by dissimilatory Fe(III)-reducing bacteria, or by metamorphic (high pressure and temperature) reactions occurring in presence of buried organic matter. Here, we present the current understanding of the role of Fe-metabolizing bacteria in the deposition of BIFs, as well as competing hypotheses that favor an abiotic model for BIF deposition. We also discuss the potential abiotic and microbial reduction of Fe(III) in BIFs after deposition. Further, we review the availability of essential nutrients (e.g. P and Ni) and their implications on early Earth biogeochemistry. Overall, the combined results of various ancient seawater analogue experiments aimed at assessing microbial iron cycling pathways, coupled with the analysis of the BIF rock record, point towards a strong biotic influence during BIF genesis.