Adaptations to energy stress dictate the ecology and evolution of the Archaea

Identification of a protein responsible for the synthesis of archaeal membrane-spanning GDGT lipids

Glycerol dibiphytanyl glycerol tetraethers (GDGTs) are archaeal monolayer membrane lipids that can provide a competitive advantage in extreme environments. Here, we identify a radical SAM protein, tetraether synthase (Tes), that participates in the synthesis of GDGTs. Attempts to generate a tes-deleted mutant in Sulfolobus acidocaldarius were unsuccessful, suggesting that the gene is essential in this organism. Heterologous expression of tes homologues leads to production of GDGT and structurally related lipids in the methanogen Methanococcus maripaludis (which otherwise does not synthesize GDGTs and lacks a tes homolog, but produces a putative GDGT precursor, archaeol). Tes homologues are encoded in the genomes of many archaea, as well as in some bacteria, in which they might be involved in the synthesis of bacterial branched glycerol dialkyl glycerol tetraethers.

Limits to the three domains of life: lessons from community assembly along an Antarctic salinity gradient

Extremophiles exist among all three domains of life; however, physiological mechanisms for surviving harsh environmental conditions differ among Bacteria, Archaea and Eukarya. Consequently, we expect that domain-specific variation of diversity and community assembly patterns exist along environmental gradients in extreme environments. We investigated inter-domain community compositional differences along a high-elevation salinity gradient in the McMurdo Dry Valleys, Antarctica. Conductivity for 24 soil samples collected along the gradient ranged widely from 50 to 8355 µS cm-1. Taxonomic richness varied among domains, with a total of 359 bacterial, 2 archaeal, 56 fungal, and 69 non-fungal eukaryotic operational taxonomic units (OTUs). Richness for bacteria, archaea, fungi, and non-fungal eukaryotes declined with increasing conductivity (all P < 0.05). Principal coordinate ordination analysis (PCoA) revealed significant (ANOSIM R = 0.97) groupings of low/high salinity bacterial OTUs, while OTUs from other domains were not significantly clustered. Bacterial beta diversity was unimodally distributed along the gradient and had a nested structure driven by species losses, whereas in fungi and non-fungal eukaryotes beta diversity declined monotonically without strong evidence of nestedness. Thus, while increased salinity acts as a stressor in all domains, the mechanisms driving community assembly along the gradient differ substantially between the domains.

Ammonia-oxidizing bacteria rather than ammonia-oxidizing archaea dominate nitrification in a nitrogen-fertilized calcareous soil

Microbe-driven nitrification is a key process that affects nitrogen (N) utilization by plants and N loss to the environment in agro-ecosystems. Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) are important microorganisms that dominate the ammonia oxidation process (the first and rate-limiting step of nitrification). Calcareous soils are widely distributed, accounting for more than 30% of the Earth's land. However, the effects of long-term N fertilization on the potential nitrification rate (PNR) and on AOA and AOB in calcareous soils are poorly understood. In this study, we comprehensively assessed the effects of N application (applied at five rates as urea with 0, 73.5, 105, 136.5 and 250 kg N ha^-1 for 12 years) on soil chemical characteristics, PNR, N use efficiency (NUE) and the community characteristics of AOB and AOA in a calcareous soil. N application rate affected AOB beta diversity more than that of AOA. Compared to no N control, N application significantly decreased the relative abundance of Group I.1b clade A of AOA and Nitrosospira cluster 3a.2 of AOB, but increased Nitrosomonas cluster 7 of AOB. The relative abundance of Nitrosospira cluster 3a.2 of AOB was negatively correlated with PNR. A structural equation model showed a direct effect of N application rate on the content of soil organic matter and nitrate, the alpha and beta diversity of AOA and AOB. Nitrate and AOB beta diversity were the key factors affecting PNR. Overall, the alpha, beta diversity and community composition of AOB contribute more to PNR than AOA in calcareous soils with high organic matter content. Understanding the relationship between the characteristics of AOA and AOB in calcareous soils and PNR will help to improve NUE.

Is the rhizosphere a source of applicable multi-beneficial microorganisms for plant enhancement?

The plant faces different pedological and climatic challenges that influence its growth and enhancement. While, plant-microbes interactions throught the rhizosphere offer several privileges to this hotspot in the service of plant, by attracting multi-beneficial mutualistic and symbiotic microorganisms as plant growth-promoting bacteria (PGPB), archaea, mycorrhizal fungi, endophytic fungi, and others…). Currently, numerous investigations showed the beneficial effects of these microbes on growth and plant health. Indeed, rhizospheric microorganisms offer to host plants the essential assimilable nutrients, stimulate the growth and development of host plants, and induce antibiotics production. They also attributed to host plants numerous phenotypes involved in the increase the resistance to abiotic and biotic stresses. The investigations and the studies on the rhizosphere can offer a way to find a biological and sustainable solution to confront these environmental problems. Therefore, the interactions between microbes and plants may lead to interesting biotechnological applications on plant improvement and the adaptation in different climates to obtain a biological sustainable agricultures without the use of chemical fertilizers.

Low membrane fluidity triggers lipid phase separation and protein segregation in living bacteria

All living organisms adapt their membrane lipid composition in response to changes in their environment or diet. These conserved membrane-adaptive processes have been studied extensively. However, key concepts of membrane biology linked to regulation of lipid composition including homeoviscous adaptation maintaining stable levels of membrane fluidity, and gel-fluid phase separation resulting in domain formation, heavily rely upon in vitro studies with model membranes or lipid extracts. Using the bacterial model organisms Escherichia coli and Bacillus subtilis, we now show that inadequate in vivo membrane fluidity interferes with essential complex cellular processes including cytokinesis, envelope expansion, chromosome replication/segregation and maintenance of membrane potential. Furthermore, we demonstrate that very low membrane fluidity is indeed capable of triggering large-scale lipid phase separation and protein segregation in intact, protein-crowded membranes of living cells; a process that coincides with the minimal level of fluidity capable of supporting growth. Importantly, the in vivo lipid phase separation is not associated with a breakdown of the membrane diffusion barrier function, thus explaining why the phase separation process induced by low fluidity is biologically reversible.

Gut non-bacterial microbiota contributing to alcohol-associated liver disease

Intestinal microbiota, dominated by bacteria, plays an important role in the occurrence and the development of alcohol-associated liver disease (ALD), which is one of the most common liver diseases around the world. With sufficient studies focusing on the gut bacterial community, chronic alcohol consumption is now known as a key factor that alters the composition of gut bacterial community, increases intestinal permeability, causes intestinal dysfunction, induces bacterial translocation, and exacerbates the process of ALD via gut-liver axis. However, gut non-bacterial communities including fungi, viruses, and archaea, which may also participate in the disease, has received little attention relative to the gut bacterial community. This paper will systematically collect the latest literatures reporting non-bacterial communities in mammalian health and disease, and review their mechanisms in promoting the development of ALD including CLEC7A pathway, Candidalysin (a peptide toxin secreted by Candida albicans), metabolites, and other chemical substances secreted or regulated by gut commensal mycobiome, virome, and archaeome, hoping to bring novel insights on our current knowledge of ALD.

Diversity of bacterium communities in saline-alkali soil in arid regions of Northwest China

BACKGROUND

The saline-alkali soil area accounts for over 1/4-1/5 of the land area in Gansu Province of China, which are mainly distributed in the north of Hexi corridor and Jingtai basin. The unique ecological environment contains unique and diverse microbial resources. The investigation of microbial diversity in saline environment is vital to comprehend the biological mechanisms of saline adaption, develop and utilize microbial resources.

RESULTS

The Illumina MiSeq sequencing method was practiced to investigate the bacterial diversity and composition in the 5 subtypes and 13 genera of saline-alkali soil in Gansu Province, China. The results from this study show that Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, and Gemmatimonadetes were the dominant bacterial groups in 13 saline soil. Proteobacteria had the greatest abundance in sulfate-type meadow solonchaks and orthic solonchaks, chloride-type orthic solonchaks and bog solonchaks, sulfate-chloride-type, chloride-sulfate-type, and sulfate-type dry solonchaks. Halobacteria was the dominant bacterial class in soil samples except for sulfate-type meadow solonchaks and orthic solonchaks, chloride-type orthic solonchaks and bog solonchaks. The richness estimators of Ace and Chao 1 and the diversity indices of Shannon and Simpson revealed the least diversity in bacterial community in sulfate-chloride-type orthic solonchaks.

CONCLUSIONS

The sulfate anion was the most important driving force for bacterial composition (17.7%), and the second most influencing factor was pH value (11.7%).

The rates of global bacterial and archaeal dispersal

The phylogenetic resolution at which microorganisms display geographic endemism, the rates at which they disperse at global scales, and the role of humans on global microbial dispersal are largely unknown. Answering these questions is necessary for interpreting microbial biogeography, ecology, and macroevolution and for predicting the spread of emerging pathogenic strains. To resolve these questions, I analyzed the geographic and evolutionary relationships between 36,795 bacterial and archaeal ("prokaryotic") genomes from ∼7000 locations around the world. I find clear signs of continental-scale endemism, including strong correlations between phylogenetic divergence and geographic distance. However, the phylogenetic scale at which endemism generally occurs is extremely small, and most "species" (defined by an average nucleotide identity ≥ 95%) and even closely related strains (average nucleotide identity ≥ 99.9%) are globally distributed. Human-associated lineages display faster dispersal rates than other terrestrial lineages; the average net distance between any two human-associated cell lineages diverging 50 years ago is roughly 580 km. These results suggest that many previously reported global-scale microbial biogeographical patterns are likely the result of recent or current environmental filtering rather than geographic endemism. For human-associated lineages, estimated transition rates between Europe and North America are particularly high, and much higher than for non-human associated terrestrial lineages, highlighting the role that human movement plays in global microbial dispersal. Dispersal was slowest for hot spring- and terrestrial subsurface-associated lineages, indicating that these environments may act as "isolated islands" of microbial evolution.

A Novel Approach to Characterize the Lipidome of Marine Archaeon Nitrosopumilus maritimus by Ion Mobility Mass Spectrometry

Archaea are differentiated from the other two domains of life by their biomolecular characteristics. One such characteristic is the unique structure and composition of their lipids. Characterization of the whole set of lipids in a biological system (the lipidome) remains technologically challenging. This is because the lipidome is innately complex, and not all lipid species are extractable, separable, or ionizable by a single analytical method. Furthermore, lipids are structurally and chemically diverse. Many lipids are isobaric or isomeric and often indistinguishable by the measurement of mass or even their fragmentation spectra. Here we developed a novel analytical protocol based on liquid chromatography ion mobility mass spectrometry to enhance the coverage of the lipidome and characterize the conformations of archaeal lipids by their collision cross-sections (CCSs). The measurements of ion mobility revealed the gas-phase ion chemistry of representative archaeal lipids and provided further insights into their attributions to the adaptability of archaea to environmental stresses. A comprehensive characterization of the lipidome of mesophilic marine thaumarchaeon, Nitrosopumilus maritimus (strain SCM1) revealed potentially an unreported phosphate- and sulfate-containing lipid candidate by negative ionization analysis. It was the first time that experimentally derived CCS values of archaeal lipids were reported. Discrimination of crenarchaeol and its proposed stereoisomer was, however, not achieved with the resolving power of the SYNAPT G2 ion mobility system, and a high-resolution ion mobility system may be required for future work. Structural and spectral libraries of archaeal lipids were constructed in non-vendor-specific formats and are being made available to the community to promote research of Archaea by lipidomics.

Going Beyond Bacteria: Uncovering the Role of Archaeome and Mycobiome in Inflammatory Bowel Disease

Inflammatory Bowel Disease (IBD) is a multifaceted class of relapsing-remitting chronic inflammatory conditions where microbiota dysbiosis plays a key role during its onset and progression. The human microbiota is a rich community of bacteria, viruses, fungi, protists, and archaea, and is an integral part of the body influencing its overall homeostasis. Emerging evidence highlights dysbiosis of the archaeome and mycobiome to influence the overall intestinal microbiota composition in health and disease, including IBD, although they remain some of the least understood components of the gut microbiota. Nonetheless, their ability to directly impact the other commensals, or the host, reasonably makes them important contributors to either the maintenance of the mucosal tissue physiology or to chronic intestinal inflammation development. Therefore, the full understanding of the archaeome and mycobiome dysbiosis during IBD pathogenesis may pave the way to the discovery of novel mechanisms, finally providing innovative therapeutic targets that can soon implement the currently available treatments for IBD patients.

Lipid synthesis at the trophic base as the source for energy management to build complex structures

The review explores the ecological basis for bacterial lipid metabolism in marine and terrestrial ecosystems. We discuss ecosystem stressors that provoked early organisms to modify their lipid membrane structures, and where these stressors are found across a variety of environments. A major role of lipid membranes is to manage cellular energy utility, including how energy is used for signal propagation. As different environments are imbued with properties that necessitate variation in energy regulation, bacterial lipid synthesis has undergone incalculable permutations of functional trial and error. This may hold clues for how biotechnology can improvise a short-hand version of the evolutionary gauntlet to stimulate latent functional competences for the synthesis of rare lipids. Reducing human reliance on marine resources and deriving solutions for production of essential nutrients is a pressing problem in sustainable agriculture and aquaculture, as well as timely considering the increasing fragility of human health in an aging population.

Exploring the global vaginal microbiome and its impact on human health

Around the world, more than 175,000,000 women are diagnosed every year with gynaecological disease, in many cases contributing to high morbidity and mortality. For this reason, knowledge of the composition of the vaginal microbiome and its variations represents a real health challenge, as this is key to improving therapeutic management. This review traces the history of the poorly known vaginal microbiome and focuses on the latest findings concerning this ecosystem. Studies in the past decade have targeted complex bacterial communities within the vagina. However, due to the development of technology and the emergence of next generation sequencing (NGS), the exact definition of the vaginal microbiome has changed and can no longer be linked solely to the presence of bacteria. In order to reach a global view of the vaginal microbiome, it is essential to take into account all microorganisms that the vagina harbours, including fungi, viruses, archaea, and candidate phyla radiation. Although these communities represent only a minimal percentage of the vaginal microbiome, they may act as modifiers of its basic physiology and may play a key role in the maintenance of microbial communities, as well as metabolic and immune functions. Studies of the complex interactions between these different microorganisms have recently begun and are not yet fully understood. Results to date indicate that these microbial communities together constitute the first line of defence against infections. On the other hand, the slightest disturbance in this microbiome may lead to disease. For this reason, enhanced knowledge of these associations is critical to better identify predispositions to certain illnesses, which may open new therapeutic avenues. Currently however, only the tip of the iceberg is understood and current research on this ecosystem is revolutionising our knowledge and understanding of human health and disease.

The Evolution of the Hallmarks of Aging

The evolutionary theory of aging has set the foundations for a comprehensive understanding of aging. The biology of aging has listed and described the "hallmarks of aging," i.e., cellular and molecular mechanisms involved in human aging. The present paper is the first to infer the order of appearance of the hallmarks of bilaterian and thereby human aging throughout evolution from their presence in progressively narrower clades. Its first result is that all organisms, even non-senescent, have to deal with at least one mechanism of aging - the progressive accumulation of misfolded or unstable proteins. Due to their cumulation, these mechanisms are called "layers of aging." A difference should be made between the first four layers of unicellular aging, present in some unicellular organisms and in all multicellular opisthokonts, that stem and strike "from the inside" of individual cells and span from increasingly abnormal protein folding to deregulated nutrient sensing, and the last four layers of metacellular aging, progressively appearing in metazoans, that strike the cells of a multicellular organism "from the outside," i.e., because of other cells, and span from transcriptional alterations to the disruption of intercellular communication. The evolution of metazoans and eumetazoans probably solved the problem of aging along with the problem of unicellular aging. However, metacellular aging originates in the mechanisms by which the effects of unicellular aging are kept under control - e.g., the exhaustion of stem cells that contribute to replace damaged somatic cells. In bilaterians, additional functions have taken a toll on generally useless potentially limited lifespan to increase the fitness of organisms at the price of a progressively less efficient containment of the damage of unicellular aging. In the end, this picture suggests that geroscience should be more efficient in targeting conditions of metacellular aging rather than unicellular aging itself.

Interactions between temperature and energy supply drive microbial communities in hydrothermal sediment

Temperature and bioavailable energy control the distribution of life on Earth, and interact with each other due to the dependency of biological energy requirements on temperature. Here we analyze how temperature-energy interactions structure sediment microbial communities in two hydrothermally active areas of Guaymas Basin. Sites from one area experience advective input of thermogenically produced electron donors by seepage from deeper layers, whereas sites from the other area are diffusion-dominated and electron donor-depleted. In both locations, Archaea dominate at temperatures >45 °C and Bacteria at temperatures <10 °C. Yet, at the phylum level and below, there are clear differences. Hot seep sites have high proportions of typical hydrothermal vent and hot spring taxa. By contrast, high-temperature sites without seepage harbor mainly novel taxa belonging to phyla that are widespread in cold subseafloor sediment. Our results suggest that in hydrothermal sediments temperature determines domain-level dominance, whereas temperature-energy interactions structure microbial communities at the phylum-level and below.

Lagostina et al. show that relative abundances of Bacteria and Archaea in sediments of Guaymas Basin, Gulf of California, are controlled by temperature, while energy flux explains microbial community structure at the phylum-level and below. Hot diffusion-dominated and energy-depleted sediments are dominated by taxa with relatives in cold subseafloor sediments, while hot sediments with high energy supply from fluid seepage are dominated by taxa also found at hydrothermal vents and in hot springs.

The biology of thermoacidophilic archaea from the order Sulfolobales

Thermoacidophilic archaea belonging to the order Sulfolobales thrive in extreme biotopes, such as sulfuric hot springs and ore deposits. These microorganisms have been model systems for understanding life in extreme environments, as well as for probing the evolution of both molecular genetic processes and central metabolic pathways. Thermoacidophiles, such as the Sulfolobales, use typical microbial responses to persist in hot acid (e.g. motility, stress response, biofilm formation), albeit with some unusual twists. They also exhibit unique physiological features, including iron and sulfur chemolithoautotrophy, that differentiate them from much of the microbial world. Although first discovered >50 years ago, it was not until recently that genome sequence data and facile genetic tools have been developed for species in the Sulfolobales. These advances have not only opened up ways to further probe novel features of these microbes but also paved the way for their potential biotechnological applications. Discussed here are the nuances of the thermoacidophilic lifestyle of the Sulfolobales, including their evolutionary placement, cell biology, survival strategies, genetic tools, metabolic processes and physiological attributes together with how these characteristics make thermoacidophiles ideal platforms for specialized industrial processes.

K fertilizer alleviates N2O emissions by regulating the abundance of nitrifying and denitrifying microbial communities in the soil-plant system

Potassium (K) fertilizer additions can result in high crop yields of good quality and low nitrogen (N) loss; however, the interaction between K and N fertilizer and its effect on N₂O emissions and associated microbes remain unclear. We investigated this in a pot experiment with six fertilizer treatments involving K and two sources of N, using agricultural soil from the suburbs of Wuhan, central China. The aim was to determine the effects of the interaction between K and different forms of N on the N₂O flux and the abundance of nitrifying and denitrifying microbial communities, using static chamber-gas chromatography and high-throughput sequencing methods. Compared with no fertilizer control (CK), the addition of nitrate fertilizer (NN) or ammonia fertilizer (AN) or K fertilizer significantly increased N₂O emissions. However, the combined application (NNK) of K and NN significantly reduced the average N₂O emissions by 28.3%, while the combined application (ANK) of K and AN increased N₂O emissions by 22.7%. The abundance of nitrifying genes amoA in ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) changed in response to N and/or K fertilization, but the denitrifying genes narG, nirK and norl were strongly correlated with N₂O emissions. This suggests that N or K fertilizer and their interaction affect N₂O emissions mainly by altering the abundance of functional genes of denitrifying microbes in the soil-plant system. The genera Paracoccus, Rubrivivax and Geobacter as well as Streptomyces and Hyphomicrobium play an important role in N₂O emissions during denitrification with the combined application of N and K.

Self-Assembling Peptidic Bolaamphiphiles for Biomimetic Applications

Bolaamphiphile, which is a class of amphiphilic molecules, has a unique structure of two hydrophilic head groups at the ends of the hydrophobic center. Peptidic bolaamphiphiles that employ peptides or amino acids as their hydrophilic groups exhibit unique biochemical activities when they self-organize into supramolecular structures, which are not observed in a single molecule. The self-assembled peptidic bolaamphiphiles hold considerable promise for imitating proteins with biochemical activities, such as specific affinity toward heterogeneous substances, a catalytic activity similar to a metalloenzyme, physicochemical activity from harmonized amino acid segments, and the capability to encapsulate genes like a viral vector. These diverse activities give rise to large research interest in biomaterials engineering, along with the synthesis and characterization of the assembled structures. This review aims to address the recent progress in the applications of peptidic bolaamphiphile assemblies whose densely packed peptide motifs on their surface and their stacked hydrophobic centers exhibit unique protein-like activity and designer functionality, respectively.

The histone chaperone HIR maintains chromatin states to control nitrogen assimilation and fungal virulence

Adaptation to changing environments and immune evasion is pivotal for fitness of pathogens. Yet, the underlying mechanisms remain largely unknown. Adaptation is governed by dynamic transcriptional re-programming, which is tightly connected to chromatin architecture. Here, we report a pivotal role for the HIR histone chaperone complex in modulating virulence of the human fungal pathogen Candida albicans. Genetic ablation of HIR function alters chromatin accessibility linked to aberrant transcriptional responses to protein as nitrogen source. This accelerates metabolic adaptation and increases the release of extracellular proteases, which enables scavenging of alternative nitrogen sources. Furthermore, HIR controls fungal virulence, as HIR1 deletion leads to differential recognition by immune cells and hypervirulence in a mouse model of systemic infection. This work provides mechanistic insights into chromatin-coupled regulatory mechanisms that fine-tune pathogen gene expression and virulence. Furthermore, the data point toward the requirement of refined screening approaches to exploit chromatin modifications as antifungal strategies.

Comparative Genomics Provides Insights into the Genetic Diversity and Evolution of the DPANN Superphylum

DPANN is known as highly diverse, globally widespread, and mostly ectosymbiotic archaeal superphylum. However, this group of archaea was overlooked for a long time, and there were limited in-depth studies reported. In this investigation, 41 metagenome-assembled genomes (MAGs) belonging to the DPANN superphylum were recovered (18 MAGs had average nucleotide identity [ANI] values of <95% and a percentage of conserved proteins [POCP] of >50%, while 14 MAGs showed a POCP of <50%), which were analyzed comparatively with 515 other published DPANN genomes. Mismatches to known 16S rRNA gene primers were identified among 16S rRNA genes of DPANN archaea. Numbers of gene families lost (mostly related to energy and amino acid metabolism) were over three times greater than those gained in the evolution of DPANN archaea. Lateral gene transfer (LGT; ∼45.5% was cross-domain) had facilitated niche adaption of the DPANN archaea, ensuring a delicate equilibrium of streamlined genomes with efficient niche-adaptive strategies. For instance, LGT-derived cytochrome bd ubiquinol oxidase and arginine deiminase in the genomes of “Candidatus Micrarchaeota” could help them better adapt to aerobic acidic mine drainage habitats. In addition, most DPANN archaea acquired enzymes for biosynthesis of extracellular polymeric substances (EPS) and transketolase/transaldolase for the pentose phosphate pathway from Bacteria.

IMPORTANCE The domain Archaea is a key research model for gaining insights into the origin and evolution of life, as well as the relevant biogeochemical processes. The discovery of nanosized DPANN archaea has overthrown many aspects of microbiology. However, the DPANN superphylum still contains a vast genetic novelty and diversity that need to be explored. Comprehensively comparative genomic analysis on the DPANN superphylum was performed in this study, with an attempt to illuminate its metabolic potential, ecological distribution and evolutionary history. Many interphylum differences within the DPANN superphylum were found. For example, Altiarchaeota had the biggest genome among DPANN phyla, possessing many pathways missing in other phyla, such as formaldehyde assimilation and the Wood-Ljungdahl pathway. In addition, LGT acted as an important force to provide DPANN archaeal genetic flexibility that permitted the occupation of diverse niches. This study has advanced our understanding of the diversity and genome evolution of archaea.

Variation, distribution, and diversity of canonical ammonia-oxidizing microorganisms and complete-nitrifying bacteria in highly contaminated ecological restoration regions in the Siding mine area

Canonical ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and complete-nitrifying bacteria (comammox) exist in a variety of ecosystems. However, little is known about AOA, AOB and comammox or their contributions to nitrification in the soils of heavily degraded and acidic mine regions. In the present study, the activity, richness, diversity and distribution patterns of AOA, AOB and comammox in the Siding mine area were investigated. Nemerow's multifactor pollution index (P_N) values indicated that the soil in all three areas in the Siding mine area was highly contaminated by Cd, Pb, Zn, Mn and Cu. The AOA, AOB and comammox amoA gene copy numbers exhibited significant positive correlations with Pb and Zn levels and P_N values, which indicated that the populations of AOA, AOB and comammox underwent adaptation and reproduction in response to pollution from multiple metals in the Siding mine area. Among them, the abundance of AOA was the highest, and AOA may survive better than AOB and comammox under such severely pollution-stressed and ammonia-limited conditions. The phyla Thaumarchaeota and Crenarchaeota may play vital roles in the soil ammonia oxidation process. Unlike AOA, AOB may use soil available phosphorus to help them compete for NH₃ and other limiting nutrients with AOA and heterotrophs. Moreover, soil organic matter was the main factor influencing the species diversity of AOB, the β-diversity of AOB and comammox, and the community composition of AOA, AOB and comammox. Our research will help to explain the role and importance of AOA, AOB and comammox in the different ecological restoration regions in the Siding mine area.

Life in hot acid: a genome-based reassessment of the archaeal order Sulfolobales

The order Sulfolobales was one of the first named Archaeal lineages, with globally distributed members from terrestrial thermal acid springs (pH < 4; T > 65°C). The Sulfolobales represent broad metabolic capabilities, ranging from lithotrophy, based on inorganic iron and sulfur biotransformations, to autotrophy, to chemoheterotrophy in less acidophilic species. Components of the 3-hydroxypropionate/4-hydroxybutyrate carbon fixation cycle, as well as sulfur oxidation, are nearly universally conserved, although dissimilatory sulfur reduction and disproportionation (Acidianus, Stygiolobus and Sulfurisphaera) and iron oxidation (Acidianus, Metallosphaera, Sulfurisphaera, Sulfuracidifex and Sulfodiicoccus) are limited to fewer lineages. Lithotrophic marker genes appear more often in highly acidophilic lineages. Despite the presence of facultative anaerobes and one confirmed obligate anaerobe, oxidase complexes (fox, sox, dox and a new putative cytochrome bd) are prevalent in many species (even facultative/obligate anaerobes), suggesting a key role for oxygen among the Sulfolobales. The presence of fox genes tracks with a putative antioxidant OsmC family peroxiredoxin, an indicator of oxidative stress derived from mixing reactive metals and oxygen. Extreme acidophily appears to track inversely with heterotrophy but directly with lithotrophy. Recent phylogenetic re-organization efforts are supported by the comparative genomics here, although several changes are proposed, including the expansion of the genus Saccharolobus.

Interplay of Various Evolutionary Modes in Genome Diversification and Adaptive Evolution of the Family Sulfolobaceae

Sulfolobaceae family, comprising diverse thermoacidophilic and aerobic sulfur-metabolizing Archaea from various geographical locations, offers an ideal opportunity to infer the evolutionary dynamics across the members of this family. Comparative pan-genomics coupled with evolutionary analyses has revealed asymmetric genome evolution within the Sulfolobaceae family. The trend of genome streamlining followed by periods of differential gene gains resulted in an overall genome expansion in some species of this family, whereas there was reduction in others. Among the core genes, both Sulfolobus islandicus and Saccharolobus solfataricus showed a considerable fraction of positively selected genes and also higher frequencies of gene acquisition. In contrast, Sulfolobus acidocaldarius genomes experienced substantial amount of gene loss and strong purifying selection as manifested by relatively lower genome size and higher genome conservation. Central carbohydrate metabolism and sulfur metabolism coevolved with the genome diversification pattern of this archaeal family. The autotrophic CO2 fixation with three significant positively selected enzymes from S. islandicus and S. solfataricus was found to be more imperative than heterotrophic CO2 fixation for Sulfolobaceae. Overall, our analysis provides an insight into the interplay of various genomic adaptation strategies including gene gain-loss, mutation, and selection influencing genome diversification of Sulfolobaceae at various taxonomic levels and geographical locations.

Enantioselective Total Synthesis of the Archaeal Lipid Parallel GDGT-0 (Isocaldarchaeol)*

Archaeal glycerol dibiphytanyl glycerol tetraethers (GDGT) are some of the most unusual membrane lipids identified in nature. These amphiphiles are the major constituents of the membranes of numerous Archaea, some of which are extremophilic organisms. Due to their unique structures, there has been significant interest in studying both the biophysical properties and the biosynthesis of these molecules. However, these studies have thus far been hampered by limited access to chemically pure samples. Herein, we report a concise and stereoselective synthesis of the archaeal tetraether lipid parallel GDGT-0 and the synthesis and self-assembly of derivatives bearing different polar groups.

Effects of humic acid modified oyster shell addition on lignocellulose degradation and nitrogen transformation during digestate composting

The aim of this work was to investigate the performance of a novel humic acid modified oyster shell (MOS) bulking agent on the digestate composting. MOS was prepared by immobilizing humic acid onto oyster shell using solid phase grafting method, and then applied to the composting process. Results showed more obvious degradation of lignocellulose was observed in the MOS treatment, which was probably due to the high relative abundance of Actinobacteria. Moreover, the addition of MOS could significantly preserve NH₄⁺ and reduce the NO₃^- generation with the decreasing abundance of ammonia-oxidizing bacteria and archaea. Besides, adding MOS reduced the N₂O emission by 59.63% compared with the control. After composting, excitation-emission matrix fluorescence spectra demonstrated that the humification degree as well as compost maturity was enhanced with MOS added.

Physiological Characterization of Sulfolobus acidocaldarius in a Controlled Bioreactor Environment

The crenarchaeal model organism Sulfolobus acidocaldarius is typically cultivated in shake flasks. Although shake flasks represent the state-of-the-art for the cultivation of this microorganism, in these systems crucial process parameters, like pH or substrate availability, are only set initially, but cannot be controlled during the cultivation process. As a result, a thorough characterization of growth parameters under controlled conditions is still missing for S. acidocaldarius. In this study, we conducted chemostat cultivations at 75 °C using a growth medium containing L-glutamate and D-glucose as main carbon sources. Different pH values and dilution rates were applied with the goal to physiologically characterize the organism in a controlled bioreactor environment. Under these controlled conditions a pH optimum of 3.0 was determined. Washout of the cells occurred at a dilution rate of 0.097 h⁻¹ and the optimal productivity of biomass was observed at a dilution rate of 0.062 h⁻¹. While both carbon sources were taken up by S. acidocaldarius concomitantly, a 6.6-fold higher affinity for L-glutamate was shown. When exposed to suboptimal growth conditions, S. acidocaldarius reacted with a change in the respiratory behavior and an increased trehalose production rate in addition to a decreased growth rate.

Exposure to 1-Butanol Exemplifies the Response of the Thermoacidophilic Archaeon Sulfolobus acidocaldarius to Solvent Stress

Sulfolobus acidocaldarius is a thermoacidophilic crenarchaeon with optimal growth at 80°C and pH 2 to 3. Due to its unique physiological properties, allowing life at environmental extremes, and the recent availability of genetic tools, this extremophile has received increasing interest for biotechnological applications. In order to elucidate the potential of tolerating process-related stress conditions, we investigated the response of S. acidocaldarius toward the industrially relevant organic solvent 1-butanol. In response to butanol exposure, biofilm formation of S. acidocaldarius was enhanced and occurred at up to 1.5% (vol/vol) 1-butanol, while planktonic growth was observed at up to 1% (vol/vol) 1-butanol. Confocal laser-scanning microscopy revealed that biofilm architecture changed with the formation of denser and higher tower-like structures. Concomitantly, changes in the extracellular polymeric substances with enhanced carbohydrate and protein content were determined in 1-butanol-exposed biofilms. Using scanning electron microscopy, three different cell morphotypes were observed in response to 1-butanol. Transcriptome and proteome analyses were performed comparing the response of planktonic and biofilm cells in the absence and presence of 1-butanol. In response to 1% (vol/vol) 1-butanol, transcript levels of genes encoding motility and cell envelope structures, as well as membrane proteins, were reduced. Cell division and/or vesicle formation were upregulated. Furthermore, changes in immune and defense systems, as well as metabolism and general stress responses, were observed. Our findings show that the extreme lifestyle of S. acidocaldarius coincided with a high tolerance to organic solvents. This study provides what may be the first insights into biofilm formation and membrane/cell stress caused by organic solvents in S. acidocaldarius IMPORTANCE Archaea are unique in terms of metabolic and cellular processes, as well as the adaptation to extreme environments. In the past few years, the development of genetic systems and biochemical, genetic, and polyomics studies has provided deep insights into the physiology of some archaeal model organisms. In this study, we used S. acidocaldarius, which is adapted to the two extremes of low pH and high temperature, to study its tolerance and robustness as well as its global cellular response toward organic solvents, as exemplified by 1-butanol. We were able to identify biofilm formation as a primary cellular response to 1-butanol. Furthermore, the triggered cell/membrane stress led to significant changes in culture heterogeneity accompanied by changes in central cellular processes, such as cell division and cellular defense systems, thus suggesting a global response for the protection at the population level.

An alternative resource allocation strategy in the chemolithoautotrophic archaeon Methanococcus maripaludis

Most microorganisms in nature spend the majority of time in a state of slow or zero growth and slow metabolism under limited energy or nutrient flux rather than growing at maximum rates. Yet, most of our knowledge has been derived from studies on fast-growing bacteria. Here, we systematically characterized the physiology of the methanogenic archaeon Methanococcus maripaludis during slow growth. M. maripaludis was grown in continuous culture under energy (formate)-limiting conditions at different dilution rates ranging from 0.09 to 0.002 h^-1, the latter corresponding to 1% of its maximum growth rate under laboratory conditions (0.23 h^-1). While the specific rate of methanogenesis correlated with growth rate as expected, the fraction of cellular energy used for maintenance increased and the maintenance energy per biomass decreased at slower growth. Notably, proteome allocation between catabolic and anabolic pathways was invariant with growth rate. Unexpectedly, cells maintained their maximum methanogenesis capacity over a wide range of growth rates, except for the lowest rates tested. Cell size, cellular DNA, RNA, and protein content as well as ribosome numbers also were largely invariant with growth rate. A reduced protein synthesis rate during slow growth was achieved by a reduction in ribosome activity rather than via the number of cellular ribosomes. Our data revealed a resource allocation strategy of a methanogenic archaeon during energy limitation that is fundamentally different from commonly studied versatile chemoheterotrophic bacteria such as E. coli.

Membrane transporter dimerization driven by differential lipid solvation energetics of dissociated and associated states

Over two-thirds of integral membrane proteins of known structure assemble into oligomers. Yet, the forces that drive the association of these proteins remain to be delineated, as the lipid bilayer is a solvent environment that is both structurally and chemically complex. In this study, we reveal how the lipid solvent defines the dimerization equilibrium of the CLC-ec1 Cl^-/H⁺ antiporter. Integrating experimental and computational approaches, we show that monomers associate to avoid a thinned-membrane defect formed by hydrophobic mismatch at their exposed dimerization interfaces. In this defect, lipids are strongly tilted and less densely packed than in the bulk, with a larger degree of entanglement between opposing leaflets and greater water penetration into the bilayer interior. Dimerization restores the membrane to a near-native state and therefore, appears to be driven by the larger free-energy cost of lipid solvation of the dissociated protomers. Supporting this theory, we demonstrate that addition of short-chain lipids strongly shifts the dimerization equilibrium toward the monomeric state, and show that the cause of this effect is that these lipids preferentially solvate the defect. Importantly, we show that this shift requires only minimal quantities of short-chain lipids, with no measurable impact on either the macroscopic physical state of the membrane or the protein's biological function. Based on these observations, we posit that free-energy differentials for local lipid solvation define membrane-protein association equilibria. With this, we argue that preferential lipid solvation is a plausible cellular mechanism for lipid regulation of oligomerization processes, as it can occur at low concentrations and does not require global changes in membrane properties.

A cell’s outer membrane is made of molecules called lipids, which band together to form a flexible thin film, just two molecules thick. This membrane is dotted with proteins that transport materials in to and out of cells. Most of these membrane proteins join with other proteins to form structures known as oligomers. Except, how membrane-bound proteins assemble into oligomers – the physical forces driving these molecules to take shape – remains unclear.

This is partly because the structural, physical and chemical properties of fat-like lipid membranes are radically different to the cell’s watery interior. Consequently, the conditions under which membrane oligomers form are distinct from those surrounding proteins inside cells. Membrane proteins are also more difficult to study and characterize than water-soluble proteins inside the cell, and yet many therapeutic drugs such as antibiotics specifically target membrane proteins. Overall, our understanding of how the unique properties of lipid membranes affect the formation of protein structures embedded within, is lacking and warrants further investigation.

Now, Chadda, Bernhardt et al. focused on one membrane protein, known as CLC, which tends to exist in pairs – or dimers. To understand why these proteins form dimers (a process called dimerization) Chadda, Bernhardt et al. first used computer simulations, and then validated the findings in experimental tests.

These complementary approaches demonstrated that the main reason CLC proteins ‘dimerize’ lies in their interaction with the lipid membrane, and not the attraction of one protein to its partner. When CLC proteins are on their own, they deform the surrounding membrane and create structural defects that put the membrane under strain. But when two CLC proteins join as a dimer, this membrane strain disappears – making dimerization the more stable and energetically favorable option.

Chadda, Bernhardt et al. also showed that with the addition of a few certain lipids, specifically smaller lipids, cell membranes become more tolerant of protein-induced structural changes. This might explain how cells could use various lipids to fine-tune the activity of membrane proteins by controlling how oligomers form. However, the theory needs to be examined further. Altogether, this work has provided fundamental insights into the physical forces shaping membrane-bound proteins, relevant to researchers studying cell biology and pharmacology alike.

Higher Abundance of Sediment Methanogens and Methanotrophs Do Not Predict the Atmospheric Methane and Carbon Dioxide Flows in Eutrophic Tropical Freshwater Reservoirs

Freshwater reservoirs emit greenhouse gases (GHGs) such as methane (CH₄) and carbon dioxide (CO₂), contributing to global warming, mainly when impacted by untreated sewage and other anthropogenic sources. These gases can be produced by microbial organic carbon decomposition, but little is known about the microbiota and its participation in GHG production and consumption in these environments. In this paper we analyzed the sediment microbiota of three eutrophic tropical urban freshwater reservoirs, in different seasons and evaluated the correlations between microorganisms and the atmospheric CH₄ and CO₂ flows, also correlating them to limnological variables. Our results showed that deeper water columns promote high methanogen abundance, with predominance of acetoclastic Methanosaeta spp. and hydrogenotrophs Methanoregula spp. and Methanolinea spp. The aerobic methanotrophic community was affected by dissolved total carbon (DTC) and was dominated by Crenothrix spp. However, both relative abundance of the total methanogenic and aerobic methanotrophic communities in sediments were uncoupled to CH₄ and CO₂ flows. Network based approach showed that fermentative microbiota, including Leptolinea spp. and Longilinea spp., which produces substrates for methanogenesis, influence CH₄ flows and was favored by anthropogenic pollution, such as untreated sewage loads. Additionally, less polluted conditions favored probable anaerobic methanotrophs such as Candidatus Bathyarchaeota, Sva0485, NC10, and MBG-D/DHVEG-1, which promoted lower gaseous flows, confirming the importance of sanitation improvement to reduce these flows in tropical urban freshwater reservoirs and their local and global warming impact.

Multiple environmental parameters impact lipid cyclization in Sulfolobus acidocaldarius

Adaptation of lipid membrane composition is an important component of archaeal homeostatic response. Historically, the number of cyclopentyl and cyclohexyl rings in the glycerol dibiphytanyl glycerol tetraether (GDGT) Archaeal lipids has been linked to variation in environmental temperature. However, recent work with GDGT-making archaea highlight the roles of other factors, such as pH or energy availability, in influencing the degree of GDGT cyclization. To better understand the role of multiple variables in a consistent experimental framework and organism, we cultivated the model Crenarchaeon Sulfolobus acidocaldarius DSM639 at different combinations of temperature, pH, oxygen flux, or agitation speed. We quantified responses in growth rate, biomass yield, and core lipid compositions, specifically the degree of core GDGT cyclization. The degree of GDGT cyclization correlated with growth rate under most conditions. The results suggest the degree of cyclization in archaeal lipids records a universal response to energy availability at the cellular level, both in thermoacidophiles, and in other recent findings in the mesoneutrophilic Thaumarchaea. Although we isolated the effects of key individual parameters, there remains a need for multi-factor experiments (e.g., pH + temperature + redox) in order to more robustly establish a framework to better understand homeostatic membrane responses.

Microbial production and consumption of hydrocarbons in the global ocean

Seeps, spills and other oil pollution introduce hydrocarbons into the ocean. Marine cyanobacteria also produce hydrocarbons from fatty acids, but little is known about the size and turnover of this cyanobacterial hydrocarbon cycle. We report that cyanobacteria in an oligotrophic gyre mainly produce n-pentadecane and that microbial hydrocarbon production exhibits stratification and diel cycling in the sunlit surface ocean. Using chemical and isotopic tracing we find that pentadecane production mainly occurs in the lower euphotic zone. Using a multifaceted approach, we estimate that the global flux of cyanobacteria-produced pentadecane exceeds total oil input in the ocean by 100- to 500-fold. We show that rapid pentadecane consumption sustains a population of pentadecane-degrading bacteria, and possibly archaea. Our findings characterize a microbial hydrocarbon cycle in the open ocean that dwarfs oil input. We hypothesize that cyanobacterial hydrocarbon production selectively primes the ocean's microbiome with long-chain alkanes whereas degradation of other petroleum hydrocarbons is controlled by factors including proximity to petroleum seepage.

The Molecular Basis for Life in Extreme Environments

Sampling and genomic efforts over the past decade have revealed an enormous quantity and diversity of life in Earth's extreme environments. This new knowledge of life on Earth poses the challenge of understandingits molecular basis in such inhospitable conditions, given that such conditions lead to loss of structure and of function in biomolecules from mesophiles. In this review, we discuss the physicochemical properties of extreme environments. We present the state of recent progress in extreme environmental genomics. We then present an overview of our current understanding of the biomolecular adaptation to extreme conditions. As our current and future understanding of biomolecular structure-function relationships in extremophiles requires methodologies adapted to extremes of pressure, temperature, and chemical composition, advances in instrumentation for probing biophysical properties under extreme conditions are presented. Finally, we briefly discuss possible future directions in extreme biophysics.

Microbial communities in rare earth mining soil after in-situ leaching mining

In-situ leaching technology is now widely used to exploit ion adsorption rare earth ore, which has caused serious environmental problems and deterioration of mining soil ecosystems. However, our knowledge about the influences of mining operation on the microbiota in these ecosystems is currently very limited. In this study, diversity and composition of prokaryote and ammonia-oxidizing microorganisms in rare earth mining soil after in-situ leaching practice were examined using quantitative Polymerase Chain Reaction (qPCR) and Illumina high-throughput sequencing. Results showed that in-situ leaching mining considerably impacted microbial communities of the mining soils. The abundances of bacterial, archaeal, and ammonia-oxidizing archaea (AOA) were significantly and negatively correlated with ionic rare earth elements (REEs), while their diversities were relatively stable. Total rare earth elements (TREEs) and ammonium were the strongest predictors of the bacterial community structure, and organic matter was the key factor predicting the variation in the archaeal community. Chloroflexi, Proteobacteria, Acidobacteria, and Actinobacteria were the most abundant bacterial phyla, and archaeal communities were dominated by Thaumarchaeota. Phylogenetic analysis indicated that unclassified Thaumarchaeota and Crenarchaeota were the predominant AOA groups. The non-detection of ammonia-oxidizing bacteria (AOB) and the abundance of AOA indicated that archaea rather than bacteria were predominantly responsible for ammonia oxidation in the mining soil. Network analysis demonstrated that positive interactions among microorganisms could increase their adaptability or resistance to this harsh environment. This study provides a comprehensive analysis of the prokaryotic communities and functional groups in rare earth mining soil after mining operation, as well as insight into the potential interactive mechanisms among soil microbes.

Bioactive Ether Lipids: Primordial Modulators of Cellular Signaling

The primacy of lipids as essential components of cellular membranes is conserved across taxonomic domains. In addition to this crucial role as a semi-permeable barrier, lipids are also increasingly recognized as important signaling molecules with diverse functional mechanisms ranging from cell surface receptor binding to the intracellular regulation of enzymatic cascades. In this review, we focus on ether lipids, an ancient family of lipids having ether-linked structures that chemically differ from their more prevalent acyl relatives. In particular, we examine ether lipid biosynthesis in the peroxisome of mammalian cells, the roles of selected glycerolipids and glycerophospholipids in signal transduction in both prokaryotes and eukaryotes, and finally, the potential therapeutic contributions of synthetic ether lipids to the treatment of cancer.

How Thermodynamics Illuminates Population Interactions in Microbial Communities

In traditional population models of microbial ecology, there are two central players: producers and consumers (including decomposers that depend on organic carbon). Producers support surface ecosystems by generating adenosine triphosphate (ATP) from sunlight, part of which is used to build new biomass from carbon dioxide. In contrast, the productivity of subsurface ecosystems with a limited supply of sunlight must rely on bacteria and archaea that are able generate ATP solely from chemical or electric energy to fix inorganic carbon. These “light-independent producers” are frequently not included in traditional food webs, even though they are ubiquitous in nature and interact with one another through the utilization of the by-products of others. In this review, we introduce theoretical approaches based on population dynamics that incorporate thermodynamics to highlight characteristic interactions in the microbial community of subsurface ecosystems, which may link community structures and ecosystem expansion under conditions of a limited supply of sunlight. In comparison with light-dependent producers, which compete with one another for light, the use of Gibbs free energy (chemical energy) can lead cooperative interactions among light-independent producers through the effects of the relative quantities of products and reactants on the available chemical energy, which is termed abundant resource premium. The development of a population theory that incorporates thermodynamics offers fundamental ecological insights into subsurface microbial ecosystems, which may be applied to fields of study such as environmental science/engineering, astrobiology, or the microbial ecosystems of the early earth.

The host-associated archaeome

Host-associated microbial communities have an important role in shaping the health and fitness of plants and animals. Most studies have focused on the bacterial, fungal or viral communities, but often the archaeal component has been neglected. The archaeal community, the so-called archaeome, is now increasingly recognized as an important component of host-associated microbiomes. It is composed of various lineages, including mainly Methanobacteriales and Methanomassiliicoccales (Euryarchaeota), as well as representatives of the Thaumarchaeota. Host-archaeome interactions have mostly been delineated from methanogenic archaea in the gastrointestinal tract, where they contribute to substantial methane production and are potentially also involved in disease-relevant processes. In this Review, we discuss the diversity and potential roles of the archaea associated with protists, plants and animals. We also present the current understanding of the archaeome in humans, the specific adaptations involved in interaction with the resident microbial community as well as with the host, and the roles of the archaeome in both health and disease.

Distinct Distribution of Archaea From Soil to Freshwater to Estuary: Implications of Archaeal Composition and Function in Different Environments

In addition to inhabiting extreme territories, Archaea are widely distributed in common environments spanning from terrestrial to aquatic environments. This study investigated and compared archaeal community structures from three different habitats (representing distinct environments): agriculture soils (from farming system trials FST, PA, United States), freshwater biofilms (from White Clay Creek, PA, United States), and estuary water (Chesapeake Bay, United States). High-throughput sequencing of 16S rRNA genes indicated that Thaumarchaeota, Euryarchaeota, Nanoarchaeota, Crenarchaeota, and Diapherotrites were the commonly found dominant phyla across these three environments. Similar to Bacteria, distinct community structure and distribution patterns for Archaea were observed in soils vs. freshwater vs. estuary. However, the abundance, richness, evenness, and diversity of archaeal communities were significantly greater in soils than it was in freshwater and estuarine environments. Indicator species (or amplicon sequence variants, ASVs) were identified from different nitrogen and carbon cycling archaeal groups in soils (Nitrososphaerales, Nitrosotaleales, Nitrosopumilales, Methanomassiliicoccales, Lainarchaeales), freshwater biofilms (Methanobacteria, Nitrososphaerales) and Chesapeake Bay (Marine Group II, Nitrosopumilales), suggesting the habitat-specificity of their biogeochemical contributions to different environments. Distinct functional aspects of Archaea were also confirmed by functional predictions (PICRUSt2 analysis). Further, co-occurrence network analysis indicated that only soil Archaea formed stable modules. Keystone species (ASVs) were identified mainly from Methanomassiliicoccales, Nitrososphaerales, Nitrosopumilales. Overall, these results indicate a strong habitat-dependent distribution of Archaea and their functional partitions within the local environments.

Broad spectrum antimicrobial activities from spore-forming bacteria isolated from the Vietnam Sea

The widespread occurrence of pathogenic bacteria resistant to last-line antibiotics has resulted in significant challenges in human and veterinary medicine. There is an urgent need for new antimicrobial agents that can be used to control these life threating pathogens. We report the identification of antimicrobial activities, against a broad range of bacterial pathogens, from a collection of marine-derived spore-forming bacteria. Although marine environments have been previously investigated as sources of novel antibiotics, studies on such environments are still limited and there remain opportunities for further discoveries and this study has used resources derived from an under-exploited region, the Vietnam Sea. Antimicrobial activity was assessed against a panel of Gram-positive and Gram-negative bacteria, including several multi-drug resistant pathogens. From a total of 489 isolates, 16.4% had antimicrobial activity. Of 23 shortlisted isolates with the greatest antimicrobial activity, 22 were Bacillus spp. isolates and one was a Paenibacillus polymyxa isolate. Most of the antimicrobial compounds were sensitive to proteases, indicating that they were proteins rather than secondary metabolites. The study demonstrated that marine bacteria derived from the Vietnam Sea represent a rich resource, producing antimicrobial compounds with activity against a broad range of clinically relevant bacterial pathogens, including important antibiotic resistant pathogens. Several isolates were identified that have particularly broad range activities and produce antimicrobial compounds that may have value for future drug development.

All living cells are cognitive

All living cells sense and respond to changes in external or internal conditions. Without that cognitive capacity, they could not obtain nutrition essential for growth, survive inevitable ecological changes, or correct accidents in the complex processes of reproduction. Wherever examined, even the smallest living cells (prokaryotes) display sophisticated regulatory networks establishing appropriate adaptations to stress conditions that maximize the probability of survival. Supposedly "simple" prokaryotic organisms also display remarkable capabilities for intercellular signalling and multicellular coordination. These observations indicate that all living cells are cognitive.

A brief review of anaerobic membrane bioreactors emphasizing recent advancements, fouling issues and future perspectives

This review summarizes the recent development and studies of anaerobic membrane bioreactor (AnMBR) to control fouling issues. AnMBR is an emerging waste water treatment technology mainly because of its low sludge residual, high volumetric organic removal rate, complete liquid-solid separation, better effluent quality, efficient resource recovery and the small footprint. This paper surveys the fundamental aspects of AnMBRs, including its applications, membrane configurations, and recent progress for enhanced reactor performance. Furthermore, the membrane fouling, a major restriction in the practical application of AnMBR, its mechanism and antifouling strategies like membrane cleaning, quorum quenching, ultrasonic treatment, membrane modifications, and antifouling agents are briefly discussed. Based on the review, the key issues that require urgent attention to facilitate large scale and integrated application of AnMBR technology are identified and future research perspectives relating to the prevalent issues are proposed.

Archaea, tiny helpers of land plants

Archaea are members of most microbiomes. While archaea are highly abundant in extreme environments, they are less abundant and diverse in association with eukaryotic hosts. Nevertheless, archaea are a substantial constituent of plant-associated ecosystems in the aboveground and belowground phytobiome. Only a few studies have investigated the role of archaea in plant health and its potential symbiosis in ecosystems. This review discusses recent progress in identifying how archaea contribute to plant traits such as growth, adaptation to abiotic stresses, and immune activation. We synthesized the most recent functional and molecular data on archaea, including root colonization and the volatile emission to activate plant systemic immunity. These data represent a paradigm shift in our understanding of plant-microbiota interactions.

Nanoparticle treatment of maize analyzed through the metatranscriptome: compromised nitrogen cycling, possible phytopathogen selection, and plant hormesis

BACKGROUND

The beneficial use of nanoparticle silver or nanosilver may be confounded when its potent antimicrobial properties impact non-target members of natural microbiomes such as those present in soil or the plant rhizosphere. Agricultural soils are a likely sink for nanosilver due to its presence in agrochemicals and land-applied biosolids, but a complete assessment of nanosilver's effects on this environment is lacking because the impact on the natural soil microbiome is not known. In a study assessing the use of nanosilver for phytopathogen control with maize, we analyzed the metatranscriptome of the maize rhizosphere and observed multiple unintended effects of exposure to 100 mg kg-1 nanosilver in soil during a growth period of 117 days.

RESULTS

We found several unintended effects of nanosilver which could interfere with agricultural systems in the long term. Firstly, the archaea community was negatively impacted with a more than 30% decrease in relative abundance, and as such, their involvement in nitrogen cycling and specifically, nitrification, was compromised. Secondly, certain potentially phytopathogenic fungal groups showed significantly increased abundances, possibly due to the negative effects of nanosilver on bacteria exerting natural biocontrol against these fungi as indicated by negative interactions in a network analysis. Up to 5-fold increases in relative abundance have been observed for certain possibly phytopathogenic fungal genera. Lastly, nanosilver exposure also caused a direct physiological impact on maize as illustrated by increased transcript abundance of aquaporin and phytohormone genes, overall resulting in a stress level with the potential to yield hormetically stimulated plant root growth.

CONCLUSIONS

This study indicates the occurrence of significant unintended effects of nanosilver use on corn, which could turn out to be negative to crop productivity and ecosystem health in the long term. We therefore highlight the need to include the microbiome when assessing the risk associated with nano-enabled agriculture. Video Abstract.

Role of biochar and organic substrates in enhancing the functional characteristics and microbial community in a saline soil

In sustaining the soil quality, soil salinization has become a major challenge due to the increasing salinity rate of 10% annually. Despite, the serious concerns, the influence of soil amendments on microbial communities and its related attributes have limited findings. Therefore, the present study aims to investigate the potential of three various biochars, digestate (DI), and its compost (COM) in reclamation of saline soil under closed ecosystem. The decrease in the pH was displayed by lignite char, and electrical conductivity by lignite char plus COM addition among all the treatments. The subside in Na ⁺, with a significant rise in K ⁺, was exhibited in soils amended with DI plus DI biochar as a combined ameliorate over control. The negative priming effects on native soil organic carbon (nSOC) due to the decreased substrate bioavailability, in corn straw and DI biochars ameliorates were noted. The urease and alkaline phosphatase activity were pronounced higher in COM. However, the catalase and fluorescein diacetate activity were greater in lignite char plus DI and COM respectively. The co-addition of biochar and organic substrates shifted microbial community, is in correspondence with the relative abundance of the phylum. Overall, the abundance of Firmicutes and Actinobacteria was higher in soils under a combination of lignite char with DI and COM respectively. Likely, the abundance of Euryarchaeota was dominant in the co-application of corn straw biochar and DI. Redundancy analysis revealed the intactness between bacterial genera and their metabolisms with K ⁺, and Mg ²⁺. PICRUSt disclosed the enhanced metabolic functions in soil with amalgam of DI and its biochar. The findings showed that the application of DI and its biochar mixture, as an amendment could be a better approach in the long-term reclamation of saline soil.

A Critical Review on Nitrous Oxide Production by Ammonia-Oxidizing Archaea

The continuous increase of nitrous oxide (N₂O) in the atmosphere has become a global concern because of its property as a potent greenhouse gas. Given the important role of ammonia-oxidizing archaea (AOA) in ammonia oxidation and their involvement in N₂O production, a clear understanding of the knowledge on archaeal N₂O production is necessary for global N₂O mitigation. Compared to bacterial N₂O production by ammonia-oxidizing bacteria (AOB), AOA-driven N₂O production pathways are less-well elucidated. In this Critical Review, we synthesized the currently proposed AOA-driven N₂O production pathways in combination with enzymology distinction, analyzed the role of AOA species involved in N₂O production pathways, discussed the relative contribution of AOA to N₂O production in both natural and anthropogenic environments, summarized the factors affecting archaeal N₂O yield, and compared the distinctions among approaches used to differentiate ammonia oxidizer-associated N₂O production. We, then, put forward perspectives for archaeal N₂O production and future challenges to further improve our understanding of the production pathways, putative enzymes involved and potential approaches for identification in order to potentially achieve effective N₂O mitigations.

Nitrogen combined with biochar changed the feedback mechanism between soil nitrification and Cd availability in an acidic soil

Inorganic nitrogen (N) inputs increase soil nitrification, acidification and trace metal toxicity e.g. cadmium (Cd). Biochar (B) has been widely used for metal immobilization. However, little is known about how the combination of N fertilizers with biochar (N-B) changes soil Cd availability through altering nitrification process. Here, (NH₄)₂SO₄ or CO(NH₂)₂ was applied in combination with biochar to an acidic, artificially enriched Cd contaminated soil. Not as we expected, available Cd did not increase following (NH₄)₂SO₄ or CO(NH₂)₂ addition. Nitrification and acidification of Cd contaminated soils were greatly inhibited, accompanied by elimination of ammonia-oxidizing bacteria (AOB). Exchangeable H⁺ of Cd contaminated soils was significantly lower than that of uncontaminated soils, thus inhibiting Cd itself from mobilization. N-B addition nearly halved soil available Cd and significantly increased nitrification by promoting AOB recovery. However, the restored nitrification did not cause soil acidification, due to the high buffering and slow liming effects of biochar. Available Cd continuously decreased with decreasing soil acidity and exchangeable Al. This study firstly demonstrated a feedback between soil nitrification and Cd after N application, and how biochar modified the feedback. Biochar, therefore, provides a feasible strategy for eliminating potential Cd toxicity on both soil biological and chemical processes.

The archaeal-bacterial lipid divide, could a distinct lateral proton route hold the answer?

The archaea-bacteria lipid divide is one of the big evolutionary enigmas concerning these two domains of life. In short, bacterial membranes are made of fatty-acid esters whereas archaeal ones contain isoprenoid ethers, though at present we do not have a good understanding on why they evolved differently. The lateral proton transfer mode of energy transduction in membranes posits that protons utilize the solvation layer of the membrane interface as the main route between proton pumps and ATPases, avoiding dissipation of energy to the bulk phase. In this article I present the hypothesis on a proton-transport route through the ester groups of bacterial phospholipids as an explanation for the evolutionary divergence seen between bacteria and archaea. REVIEWERS: This article was reviewed by Uri Gophna (Editorial Board member) and Víctor Sojo.

Gut Microbiota beyond Bacteria-Mycobiome, Virome, Archaeome, and Eukaryotic Parasites in IBD

The human microbiota is a diverse microbial ecosystem associated with many beneficial physiological functions as well as numerous disease etiologies. Dominated by bacteria, the microbiota also includes commensal populations of fungi, viruses, archaea, and protists. Unlike bacterial microbiota, which was extensively studied in the past two decades, these non-bacterial microorganisms, their functional roles, and their interaction with one another or with host immune system have not been as widely explored. This review covers the recent findings on the non-bacterial communities of the human gastrointestinal microbiota and their involvement in health and disease, with particular focus on the pathophysiology of inflammatory bowel disease.