Perspectives on Cultivation Strategies of Archaea

Microbial communities in the Dead Sea and their potential biotechnological applications

The Dead Sea is unique compared to other extreme halophilic habitats. Its salinity exceeds 34%, and it is getting saltier. The Dead Sea environment is characterized by a dominance of divalent cations, with magnesium chloride (MgCl2) levels approaching the predicted 2.3 M upper limit for life, an acidic pH of 6.0, and high levels of absorbed ultraviolet radiation. Consequently, only organisms adapted to such a polyextreme environment can survive in the surface, sinkholes, sediments, muds, and underwater springs of the Dead Sea. Metagenomic sequence analysis and amino acid profiling indicated that the Dead Sea is predominantly composed of halophiles that have various adaptation mechanisms and produce metabolites that can be utilized for biotechnological purposes. A variety of products have been obtained from halophilic microorganisms isolated from the Dead Sea, such as antimicrobials, bioplastics, biofuels, extremozymes, retinal proteins, colored pigments, exopolysaccharides, and compatible solutes. These resources find applications in agriculture, food, biofuel production, industry, and bioremediation for the detoxification of wastewater and soil. Utilizing halophiles as a bioprocessing platform offers advantages such as reduced energy consumption, decreased freshwater demand, minimized capital investment, and continuous production.

Fusion/fission protein family identification in Archaea

The majority of newly discovered archaeal lineages remain without a cultivated representative, but scarce experimental data from the cultivated organisms show that they harbor distinct functional repertoires. To unveil the ecological as well as evolutionary impact of Archaea from metagenomics, new computational methods need to be developed, followed by in-depth analysis. Among them is the genome-wide protein fusion screening performed here. Natural fusions and fissions of genes not only contribute to microbial evolution but also complicate the correct identification and functional annotation of sequences. The products of these processes can be defined as fusion (or composite) proteins, the ones consisting of two or more domains originally encoded by different genes and split proteins, and the ones originating from the separation of a gene in two (fission). Fusion identifications are required for proper phylogenetic reconstructions and metabolic pathway completeness assessments, while mappings between fused and unfused proteins can fill some of the existing gaps in metabolic models. In the archaeal genome-wide screening, more than 1,900 fusion/fission protein clusters were identified, belonging to both newly sequenced and well-studied lineages. These protein families are mainly associated with different types of metabolism, genetic, and cellular processes. Moreover, 162 of the identified fusion/fission protein families are archaeal specific, having no identified fused homolog within the bacterial domain. Our approach was validated by the identification of experimentally characterized fusion/fission cases. However, around 25% of the identified fusion/fission families lack functional annotations for both composite and split states, showing the need for experimental characterization in Archaea.IMPORTANCEGenome-wide fusion screening has never been performed in Archaea on a broad taxonomic scale. The overlay of multiple computational techniques allows the detection of a fine-grained set of predicted fusion/fission families, instead of rough estimations based on conserved domain annotations only. The exhaustive mapping of fused proteins to bacterial organisms allows us to capture fusion/fission families that are specific to archaeal biology, as well as to identify links between bacterial and archaeal lineages based on cooccurrence of taxonomically restricted proteins and their sequence features. Furthermore, the identification of poorly characterized lineage-specific fusion proteins opens up possibilities for future experimental and computational investigations. This approach enhances our understanding of Archaea in general and provides potential candidates for in-depth studies in the future.

The Archaea domain: Exploring historical and contemporary perspectives with in silico primer coverage analysis for future research in Dentistry

OBJECTIVE

The complete picture of how the human microbiome interacts with its host is still largely unknown, particularly concerning microorganisms beyond bacteria. Although existing in very low abundance and not directly linked to causing diseases, archaea have been detected in various sites of the human body, including the gastrointestinal tract, oral cavity, skin, eyes, respiratory and urinary systems. But what exactly are these microorganisms? In the early 1990 s, archaea were classified as a distinct domain of life, sharing a more recent common ancestor with eukaryotes than with bacteria. While archaea's presence and potential significance in Dentistry remain under-recognized, there are concerns that they may contribute to oral dysbiosis. However, detecting archaea in oral samples presents challenges, including difficulties in culturing, the selection of DNA extraction methods, primer design, bioinformatic analysis, and databases.

DESIGN

This is a comprehensive review on the oral archaeome, presenting an in-depth in silico analysis of various primers commonly used for detecting archaea in human body sites.

RESULTS

Among several primer pairs used for detecting archaea in human samples across the literature, only one specifically designed for detecting methanogenic archaea in stool samples, exhibited exceptional coverage levels for the domain and various archaea phyla.

CONCLUSIONS

Our in silico analysis underscores the need for designing new primers targeting not only methanogenic archaea but also nanoarchaeal and thaumarchaeota groups to gain a comprehensive understanding of the archaeal oral community. By doing so, researchers can pave the way for further advancements in the field of oral archaeome research.

Exploring the human archaeome: its relevance for health and disease, and its complex interplay with the human immune system

This Review aims to coalesce existing knowledge on the human archaeome, a less-studied yet critical non-bacterial component of the human microbiome, with a focus on its interaction with the immune system. Despite a largely bacteria-centric focus in microbiome research, archaea present unique challenges and opportunities for understanding human health. We examine the archaeal distribution across different human body sites, such as the lower gastrointestinal tract (LGT), upper aerodigestive tract (UAT), urogenital tract (UGT), and skin. Variability in archaeal composition exists between sites; methanogens dominate the LGT, while Nitrososphaeria are prevalent on the skin and UAT. Archaea have yet to be classified as pathogens but show associations with conditions such as refractory sinusitis and vaginosis. In the LGT, methanogenic archaea play critical metabolic roles by converting bacterial end-products into methane, correlating with various health conditions, including obesity and certain cancers. Finally, this work looks at the complex interactions between archaea and the human immune system at the molecular level. Recent research has illuminated the roles of specific archaeal molecules, such as RNA and glycerolipids, in stimulating immune responses via innate immune receptors like Toll-like receptor 8 (TLR8) and 'C-type lectin domain family 4 member E' (CLEC4E; also known as MINCLE). Additionally, metabolic by-products of archaea, specifically methane, have demonstrated immunomodulatory effects through anti-inflammatory and anti-oxidative pathways. Despite these advancements, the mechanistic underpinnings of how archaea influence immune activity remain a fertile area for further investigation.

Human associated Archaea: a neglected microbiome worth investigating

The majority of research in the field of human microbiota has predominantly focused on bacterial and fungal communities. Conversely, the human archaeome has received scant attention and remains poorly studied, despite its potential role in human diseases. Archaea have the capability to colonize various human body sites, including the gastrointestinal tract, skin, vagina, breast milk, colostrum, urinary tract, lungs, nasal and oral cavities. This colonization can occur through vertical transmission, facilitated by the transfer of breast milk or colostrum from mother to child, as well as through the consumption of dairy products, organic produce, salty foods, and fermented items. The involvement of these microorganisms in diseases, such as periodontitis, might be attributed to their production of toxic compounds and the detoxification of growth inhibitors for pathogens. However, the precise mechanisms through which these contributions occur remain incompletely understood, necessitating further studies to assess their impact on human health.

Challenges and Approaches of Culturing the Unculturable Archaea

Since Carl Woese's discovery of archaea as a third domain of life, numerous archaeal species have been discovered, yet archaeal diversity is poorly characterized. Culturing archaea is complicated, but several queries about archaeal cell biology, evolution, physiology, and diversity need to be solved by culturing and culture-dependent techniques. Increasing interest in demand for innovative culturing methods has led to various technological and methodological advances. The current review explains frequent hurdles hindering uncultured archaea isolation and discusses features for more archaeal cultivation. This review also discusses successful strategies and available media for archaeal culturing, which might be helpful for future culturing practices.

Unraveling the Endodontic Archaeome: A Systematic Review with Meta-Analysis

INTRODUCTION

The controversial issue of whether the Archaea domain plays a role in endodontic infections is the focus of this systematic review with meta-analysis. The aim is to emphasize the significance of minority microbial domains in oral dysbiosis by evaluating the prevalence of archaea in root canals and its association with clinical parameters such as symptomatology and type of endodontic infection.

METHODS

The search strategy involved researching 6 databases and the gray literature. Publications were accepted in any year or language that identified archaea in samples from endodontic canals. A 2-step selection process narrowed the final choice to 16 articles. The methodological quality of the studies was evaluated using tools from the Joanna Briggs Institute, and the certainty of evidence was assessed using the Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) approach.

RESULTS

The results showed that archaea were present in 20% (95% [confidence interval] CI = 8%-32%) of individuals with endodontic samples analyzed. The samples were about twice as likely to be archaeal-positive if collected from individuals with primary vs. persistent/secondary infection (odds ratio = 2.33; 95% CI = 1.31-4.14; I2 = 0%), or individuals with self-reported vs. symptom-free infections (odds ratio = 2.67; 95% CI = 1.47-4.85; I2 = 0%). Methanogenic archaea were reported in 66% of the included studies. Representative members of phyla Thaumarchaeota and Crenarchaeota were also identified.

CONCLUSIONS

Archaea are present in about one-fifth of the infected root canals. Recognized biases in experimental approaches for researching archaea must be addressed to understand the prevalence and roles of archaea in endodontic infections, and to determine whether the decontamination process should include the elimination or neutralization of archaea from root canals (International Prospective Register of Systematic Reviews protocol = CRD42021264308).

Study of Archaeal Diversity in the Arctic Meltwater Lake Region

Two typical lakes formed from meltwater in the Ny-Ålesund area were taken as the study subjects in 2018. To investigate the archaeal community compositions of the two lakes, 16S rRNA genes from soil samples from the intertidal and subtidal zones of the two lakes were sequenced with high throughput. At the phylum level, the intertidal zone was dominated by Crenarchaeota and the subtidal zone was dominated by Halobacter; at the genus level, the intertidal zone was dominated by Nitrososphaeraceae_unclassified and Candidatus_Nitrocosmicus, while the subtidal zone was dominated by Methanoregula. The soil physicochemical factors pH, moisture content (MC), total organic carbon (TOC), total organic nitrogen (TON), nitrite nitrogen (NO₂^--N), and nitrate nitrogen (NO₃^--N) were significantly different in the intertidal and subtidal zones of the lake. By redundancy analysis, the results indicated that NH₄⁺-N, SiO₃^2--Si, MC, NO₃^--N, and NO₂^--N have had highly significant effects on the archaeal diversity and distribution. A weighted gene co-expression network analysis (WGCNA) was used to search for hub archaea associated with physicochemical factors. The results suggested that these physicochemical factors play important roles in the diversity and structure of the archaeal community at different sites by altering the abundance of certain hub archaea. In addition, Woesearchaeales was found to be the hub archaea genus at every site.

Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles

More than 20,000 species of prokaryotes (less than 1% of the estimated number of Earth's microbial species) have been described thus far. However, the vast majority of microbes that inhabit extreme environments remain uncultured and this group is termed "microbial dark matter." Little is known regarding the ecological functions and biotechnological potential of these underexplored extremophiles, thus representing a vast untapped and uncharacterized biological resource. Advances in microbial cultivation approaches are key for a detailed and comprehensive characterization of the roles of these microbes in shaping the environment and, ultimately, for their biotechnological exploitation, such as for extremophile-derived bioproducts (extremozymes, secondary metabolites, CRISPR Cas systems, and pigments, among others), astrobiology, and space exploration. Additional efforts to enhance culturable diversity are required due to the challenges imposed by extreme culturing and plating conditions. In this review, we summarize methods and technologies used to recover the microbial diversity of extreme environments, while discussing the advantages and disadvantages associated with each of these approaches. Additionally, this review describes alternative culturing strategies to retrieve novel taxa with their unknown genes, metabolisms, and ecological roles, with the ultimate goal of increasing the yields of more efficient bio-based products. This review thus summarizes the strategies used to unveil the hidden diversity of the microbiome of extreme environments and discusses the directions for future studies of microbial dark matter and its potential applications in biotechnology and astrobiology.

Characterization of the archaeal community in foods: The neglected part of the food microbiota

Despite the large number of studies conducted on archaea associated with extreme environments, the archaeal community composition in food products is still poorly known. Here, we investigated a new insight into exploring the archaeal community in several food matrices, with a particular focus on determining whether living archaea were present. A total of 71 samples of milk, cheese and its derived brine, honey, hamburger, clam, and trout were analyzed by high-throughput 16S rRNA sequencing. Archaea were detected in all the samples, ranging from 0.62 % of microbial communities in trout to 37.71 % in brine. Methanogens dominated 47.28 % of the archaeal communities, except for brine, which was dominated by halophilic taxa affiliated with the genus Haloquadratum (52.45 %). Clams were found to be a food with high richness and diversity of archaea and were targeted for culturing living archaea under different incubation time and temperature conditions. A subset of 16 communities derived from culture-dependent and culture-independent communities were assessed. Among the homogenates and living archaeal communities, the predominant taxa were distributed in the genera Nitrosopumilus (47.61 %) and Halorussus (78.78 %), respectively. A comparison of the 28 total taxa obtained by culture-dependent and culture-independent methods enabled their categorization into different groups, including detectable (8 out of 28), cultivable (8 out of 28), and detectable-cultivable (12 out of 28) taxa. Furthermore, using the culture method, the majority (14 out of 20) of living taxa grew at lower temperatures of 22 and 4 °C during long-term incubation, and few taxa (2 out of 20) were found at 37 °C during the initial days of incubation. Our results demonstrated the distribution of archaea in all analyzed food matrices, which opens new perspectives to expand our knowledge on archaea in foods and their beneficial and detrimental effects.

Diversity and structure of bacterial and archaeal communities associated with the vulnerable sponge Halichondria cebimarensis

Sponges are essential components of the marine benthos and well known for their complex and abundant associated microbial communities. There are five endemic species of the genus Halichondria on the Brazilian coast and H. cebimarensis is one of the least studied. This sponge has a very limited geographic distribution and is classified as vulnerable. In order to understand the bacterial and archaeal communities associated with this sponge, samples of H. cebimarensis were collected from the southwestern Atlantic coast (Brazil, São Paulo state). Choanosome samples were separated and processed to be (i) inoculated in three different culture media; (ii) investigated by transmission electron microscopy; (iii) submitted to 16S rRNA metabarcoding. Forty isolates were obtained and 12 were identified as belonging to the Bacilli class. The culture-dependent approaches allowed us to access unique members of the microbial community. Our analyses revealed that this animal belongs to the Low Microbial Abundance group of sponges. Culture-independent approaches showed that the H. cebimarensis microbiome is dominated by the heterotrophic Gammaproteobacteria AqS2 ("Ca. Amphirhobacter heronislandensis"). This is the first study to reveal details of the microbiome of this vulnerable sponge and is an important step in understanding how this sponge functions, its biotechnological potential and a contribution to conservation efforts.

Hydraulic retention time and pressure affect anaerobic digestion process treating synthetic glucose wastewater

High-pressure anaerobic digestion (HPAD) can directly upgrade biogas (CH₄ content to 90 %) within a reactor. Understanding of how HPAD-related microbiomes are constructed by operational parameters (hydraulic retention time (HRT) and pressure) and their interactions within the biochemical process remain underexplored. In this study, an HPAD reactor was operated at five different HRT (from 40 to 13 d), with pressure around 10-13 bar. In HPAD, pressure was the driving force behind CH₄ content. Low HRTs (13-20 d) for HPAD led to volatile fatty acids accumulation, which occurred earlier than that in normal-pressure digestion. HRT mainly affected the archaeal community, whereas pressure mostly affected the bacterial community. Hydrogenotrophic methanogen Methanobacterium prevailed at low HRTs (13-20 d). When operating continuous HPAD, attention should be paid to HRT optimization, as low HRTs (e.g., 13 d) impaired the activity of CH₄-synthesizing enzyme Methyl-coenzyme M reductase.

The Overlooked Microbiome-Considering Archaea and Eukaryotes Using Multiplex Nanopore-16S-/18S-rDNA-Sequencing: A Technical Report Focusing on Nasopharyngeal Microbiomes

In contrast to bacteria, microbiome analyses often neglect archaea, but also eukaryotes. This is partly because they are difficult to culture due to their demanding growth requirements, or some even have to be classified as uncultured microorganisms. Consequently, little is known about the relevance of archaea in human health and diseases. Contemporary broad availability and spread of next generation sequencing techniques now enable a stronger focus on such microorganisms, whose cultivation is difficult. However, due to the enormous evolutionary distances between bacteria, archaea and eukaryotes, the implementation of sequencing strategies for smaller laboratory scales needs to be refined to achieve as a holistic view on the microbiome as possible. Here, we present a technical approach that enables simultaneous analyses of archaeal, bacterial and eukaryotic microbial communities to study their roles in development and courses of respiratory disorders. We thus applied combinatorial 16S-/18S-rDNA sequencing strategies for sequencing-library preparation. Considering the lower total microbiota density of airway surfaces, when compared with gut microbiota, we optimized the DNA purification workflow from nasopharyngeal swab specimens. As a result, we provide a protocol that allows the efficient combination of bacterial, archaeal, and eukaryotic libraries for nanopore-sequencing using Oxford Nanopore Technologies MinION devices and subsequent phylogenetic analyses. In a pilot study, this workflow allowed the identification of some environmental archaea, which were not correlated with airway microbial communities before. Moreover, we assessed the protocol's broader applicability using a set of human stool samples. We conclude that the proposed protocol provides a versatile and adaptable tool for combinatorial studies on bacterial, archaeal, and eukaryotic microbiomes on a small laboratory scale.

Microbial active functional modules derived from network analysis and metabolic interactions decipher the complex microbiome assembly in mangrove sediments

BACKGROUND

The metabolic interactions of microbes significantly affect the assembly of microbial communities that play important roles in biogeochemical processes. However, most interspecies interactions between microorganisms in natural communities remain unknown, leading to a poor understanding of community assembly mechanisms.

RESULTS

Here, we used a genome-scale metabolic modeling-based approach to explore the potential interactions among bacteria and archaea in mangrove sediments. More than half of the assembled microbial species ([Formula: see text]) combined about 3000 pairwise metabolic interaction relationship with high potential. The examples of predicted interactions are consistent with the implications of studies based on microbial enrichment/culture, indicating the feasibility of our strategy for extracting diverse potential interactions from complex interspecies networks. Moreover, a substantial number of previously unknown microbial metabolic interactions were also predicted. We proposed a concept of microbial active functional module (mAFM), defined as a consortium constituted by a group of microbes possessing relatively high metabolic interactions via which they can actively realize certain dominant functions in element transformations. Based on the metabolic interactions and the transcript distribution of microorganisms, five mAFMs distributed in different layers of the sediments were identified. The whole group of mAFMs covered most of the principal pathways in the cycle of carbon, nitrogen, and sulfur, while each module possessed divergently dominant functions. According to thinctiis diston, we inferred that the mAFMs participated in the element cycles via their intra-cycle and the inter-exchange among them and the sediments.

CONCLUSIONS

The results of this study greatly expanded interaction potential of microbes in mangrove sediments, which could provide supports for prospective mutualistic system construction and microbial enrichment culture. Furthermore, the mAFMs can help to extract valuable microbial metabolic interactions from the whole community and to profile the functioning of the microbial community that promote biogeochemical cycling in mangrove sediments. Video Abstract.

Longitudinal analysis of the Five Sisters hot springs in Yellowstone National Park reveals a dynamic thermoalkaline environment

Research focused on microbial populations of thermoalkaline springs has been driven in a large part by the lure of discovering functional enzymes with industrial applications in high-pH and high temperature environments. While several studies have focused on understanding the fundamental ecology of these springs, the small molecule profiles of thermoalkaline springs have largely been overlooked. To better understand how geochemistry, small molecule composition, and microbial communities are connected, we conducted a three-year study of the Five Sisters (FS) springs that included high-resolution geochemical measurements, 16S rRNA sequencing of the bacterial and archaeal community, and mass spectrometry-based metabolite and extracellular small molecule characterization. Integration of the four datasets facilitated a comprehensive analysis of the interwoven thermoalkaline spring system. Over the course of the study, the microbial population responded to changing environmental conditions, with archaeal populations decreasing in both relative abundance and diversity compared to bacterial populations. Decreases in the relative abundance of Archaea were associated with environmental changes that included decreased availability of specific nitrogen- and sulfur-containing extracellular small molecules and fluctuations in metabolic pathways associated with nitrogen cycling. This multi-factorial analysis demonstrates that the microbial community composition is more closely correlated with pools of extracellular small molecules than with the geochemistry of the thermal springs. This is a novel finding and suggests that a previously overlooked component of thermal springs may have a significant impact on microbial community composition.

A Comprehensive Review on the Current Vaccines and Their Efficacies to Combat SARS-CoV-2 Variants

Since the first case of Coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019, SARS-CoV-2 infection has affected many individuals worldwide. Eventually, some highly infectious mutants-caused by frequent genetic recombination-have been reported for SARS-CoV-2 that can potentially escape from the immune responses and induce long-term immunity, linked with a high mortality rate. In addition, several reports stated that vaccines designed for the SARS-CoV-2 wild-type variant have mixed responses against the variants of concern (VOCs) and variants of interest (VOIs) in the human population. These results advocate the designing and development of a panvaccine with the potential to neutralize all the possible emerging variants of SARS-CoV-2. In this context, recent discoveries suggest the design of SARS-CoV-2 panvaccines using nanotechnology, siRNA, antibodies or CRISPR-Cas platforms. Thereof, the present comprehensive review summarizes the current vaccine design approaches against SARS-CoV-2 infection, the role of genetic mutations in the emergence of new viral variants, the efficacy of existing vaccines in limiting the infection of emerging SARS-CoV-2 variants, and efforts or challenges in designing SARS panvaccines.

Prokaryotes of renowned Karlovy Vary (Carlsbad) thermal springs: phylogenetic and cultivation analysis

BACKGROUND

The extreme conditions of thermal springs constitute a unique aquatic habitat characterized by low nutrient contents and the absence of human impacts on the microbial community composition. Thus, these springs may host phylogenetically novel microorganisms with potential use in biotechnology. With this hypothesis in mind, we examined the microbial composition of four thermal springs of the world-renowned spa town of Karlovy Vary (Carlsbad), Czechia, which differ in their temperature and chemical composition.

RESULTS

Microbial profiling using 16S rRNA gene sequencing revealed the presence of phylogenetically novel taxa at various taxonomic levels, spanning from genera to phyla. Many sequences belonged to novel classes within the phyla Hydrothermae, Altiarchaeota, Verrucomicrobia, and TA06. Cultivation-based methods employing oligotrophic media resulted in the isolation of 44 unique bacterial isolates. These include strains that withstand concentrations of up to 12% NaCl_w/v in cultivation media or survive a temperature of 100 °C, as well as hitherto uncultured bacterial species belonging to the genera Thermomonas, Paenibacillus, and Cellulomonas. These isolates harbored stress response genes that allow them to thrive in the extreme environment of thermal springs.

CONCLUSIONS

Our study is the first to analyze the overall microbial community composition of the renowned Karlovy Vary thermal springs. We provide insight into yet another level of uniqueness of these springs. In addition to their unique health benefits and cultural significance, we demonstrate that these springs harbor phylogenetically distinct microorganisms with unusual life strategies. Our findings open up avenues for future research with the promise of a deeper understanding of the metabolic potential of these microorganisms.

Culturable Bacterial Diversity from the Basaltic Subsurface of the Young Volcanic Island of Surtsey, Iceland

The oceanic crust is the world’s largest and least explored biosphere on Earth. The basaltic subsurface of Surtsey island in Iceland represents an analog of the warm and newly formed-oceanic crust and offers a great opportunity for discovering novel microorganisms. In this study, we collected borehole fluids, drill cores, and fumarole samples to evaluate the culturable bacterial diversity from the subsurface of the island. Enrichment cultures were performed using different conditions, media and temperatures. A total of 195 bacterial isolates were successfully cultivated, purified, and identified based on MALDI-TOF MS analysis and by 16S rRNA gene sequencing. Six different clades belonging to Firmicutes (40%), Gammaproteobacteria (28.7%), Actinobacteriota (22%), Bacteroidota (4.1%), Alphaproteobacteria (3%), and Deinococcota (2%) were identified. Bacillus (13.3%) was the major genus, followed by Geobacillus (12.33%), Enterobacter (9.23%), Pseudomonas (6.15%), and Halomonas (5.64%). More than 13% of the cultured strains potentially represent novel species based on partial 16S rRNA gene sequences. Phylogenetic analyses revealed that the isolated strains were closely related to species previously detected in soil, seawater, and hydrothermal active sites. The 16S rRNA gene sequences of the strains were aligned against Amplicon Sequence Variants (ASVs) from the previously published 16S rRNA gene amplicon sequence datasets obtained from the same samples. Compared with the culture-independent community composition, only 5 out of 49 phyla were cultivated. However, those five phyla accounted for more than 80% of the ASVs. Only 121 out of a total of 5642 distinct ASVs were culturable (≥98.65% sequence similarity), representing less than 2.15% of the ASVs detected in the amplicon dataset. Here, we support that the subsurface of Surtsey volcano hosts diverse and active microbial communities and that both culture-dependent and -independent methods are essential to improving our insight into such an extreme and complex volcanic environment.

Archaeal Communities: The Microbial Phylogenomic Frontier

Archaea are a unique system for investigating the diversity of life. There are the most diverse group of organisms with the longest evolutionary history of life on Earth. Phylogenomic investigations reveal the complex evolutionary history of Archaea, overturning longstanding views of the history of life. They exist in the harshest environments and benign conditions, providing a system to investigate the basis for living in extreme environments. They are frequently members of microbial communities, albeit generally rare. Archaea were central in the evolution of Eukaryotes and can be used as a proxy for studying life on other planets. Future advances will depend not only upon phylogenomic studies but also on a better understanding of isolation and cultivation techniques.

Diversity, metabolism and cultivation of archaea in mangrove ecosystems

Mangroves comprise a globally significant intertidal ecosystem that contains a high diversity of microorganisms, including fungi, bacteria and archaea. Archaea is a major domain of life that plays important roles in biogeochemical cycles in these ecosystems. In this review, the potential roles of archaea in mangroves are briefly highlighted. Then, the diversity and metabolism of archaeal community of mangrove ecosystems across the world are summarized and Bathyarchaeota, Euryarchaeota, Thaumarchaeota, Woesearchaeota, and Lokiarchaeota are confirmed as the most abundant and ubiquitous archaeal groups. The metabolic potential of these archaeal groups indicates their important ecological function in carbon, nitrogen and sulfur cycling. Finally, some cultivation strategies that could be applied to uncultivated archaeal lineages from mangrove wetlands are suggested, including refinements to traditional cultivation methods based on genomic and transcriptomic information, and numerous innovative cultivation techniques such as single-cell isolation and high-throughput culturing (HTC). These cultivation strategies provide more opportunities to obtain previously uncultured archaea.

Towards enriching and isolation of uncultivated archaea from marine sediments using a refined combination of conventional microbial cultivation methods

The archaea that can be readily cultivated in the laboratory are only a small fraction of the total diversity that exists in nature. Although molecular ecology methods, such as metagenomic sequencing, can provide valuable information independent of cell cultivation, it is only through cultivation-based experiments that they may be fully characterized, both for their physiological and ecological properties. Here, we report our efforts towards enriching and isolation of uncultivated archaea from marine sediments using a refined combination of conventional microbial cultivation methods. Initially, cells were retrieved from the sediment samples through a cell extraction procedure and the sediment-free mixed cells were then divided into different size-range fractions by successive filtration through 0.8 µm, 0.6 µm and 0.2 µm membranes. Archaeal 16S rRNA gene analyses indicated noticeable retention of different archaeal groups in different fractions. For each fraction, supplementation with a variety of defined substrates (e.g., methane, sulfate, and lignin) and stepwise dilutions led to highly active enrichment cultures of several archaeal groups with Bathyarchaeota most prominently enriched. Finally, using a roll-bottle technique, three co-cultures consisting of Bathyarchaeota (subgroup-8) and a bacterial species affiliated with either Pseudomonas or Glutamicibacter were obtained. Our results demonstrate that a combination of cell extraction, size fractionation, and roll-bottle isolation methods could be a useful protocol for the successful enrichment and isolation of numerous slow-growing archaeal groups from marine sediments.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-021-00092-0.

High Potential for Biomass-Degrading Enzymes Revealed by Hot Spring Metagenomics

Enzyme stability and activity at elevated temperatures are important aspects in biotechnological industries, such as the conversion of plant biomass into biofuels. In order to reduce the costs and increase the efficiency of biomass conversion, better enzymatic processing must be developed. Hot springs represent a treasure trove of underexplored microbiological and protein chemistry diversity. Herein, we conduct an exploratory study into the diversity of hot spring biomass-degrading potential. We describe the taxonomic diversity and carbohydrate active enzyme (CAZyme) coding potential in 71 publicly available metagenomic datasets from 58 globally distributed terrestrial geothermal features. Through taxonomic profiling, we detected a wide diversity of microbes unique to varying temperature and pH ranges. Biomass-degrading enzyme potential included all five classes of CAZymes and we described the presence or absence of genes encoding 19 glycosyl hydrolases hypothesized to be involved with cellulose, hemicellulose, and oligosaccharide degradation. Our results highlight hot springs as a promising system for the further discovery and development of thermo-stable biomass-degrading enzymes that can be applied toward generation of renewable biofuels. This study lays a foundation for future research to further investigate the functional diversity of hot spring biomass-degrading enzymes and their potential utility in biotechnological processing.

Scope of Archaea in Fish Feed: a New Chapter in Aquafeed Probiotics?

The outbreak of diseases leading to substantial loss is a major bottleneck in aquaculture. Over the last decades, the concept of using feed probiotics was more in focus to address the growth and health of cultivable aquatic organisms. The objective of this review is to provide an overview of the distinct functionality of archaea from conventional probiotics in nutrient utilization, specific caloric contribution, evading immune response and processing thermal resistance. The prime limitation of conventional probiotics is the viability of desired microbes under harsh feed processing conditions. To overcome the constraints of commercial probiotics pertaining to incompatibility towards industrial processing procedure, a super microbe, archaea, appears to be a potential alternative approach in aquaculture. The peculiarity of the archaeal cell wall provides them with heat stability and rigidity under industrial processing conditions. Besides, archaea being one of the gut microbial communities participates in various health-oriented biological functions in animals. Thus, the current review devoted that administration of archaea in aquafeed could be a promising strategy in aquaculture. Archaea may be used as a potential probiotic with the possible modes of functions and advantages over conventional probiotics in aquafeed preparation. The present review also provides the challenges associated with the use of archaea for aquaculture and a brief outline of the patents on archaea to highlight the various use of archaea in different sectors.

Functional and Molecular Characterization of the Halomicrobium sp. IBSBa Inulosucrase

Fructans are fructose-based (poly)saccharides with inulin and levan being the best-known ones. Thanks to their health-related benefits, inulin-type fructans have been under the focus of scientific and industrial communities, though mostly represented by plant-based inulins, and rarely by microbial ones. Recently, it was discovered that some extremely halophilic Archaea are also able to synthesize fructans. Here, we describe the first in-depth functional and molecular characterization of an Archaeal inulosucrase from Halomicrobium sp. IBSBa (HmcIsc). The HmcIsc enzyme was recombinantly expressed and purified in Escherichia coli and shown to synthesize inulin as proven by nuclear magnetic resonance (NMR) analysis. In accordance with the halophilic lifestyle of its native host, the enzyme showed maximum activity at very high NaCl concentrations (3.5 M), with specific adaptations for that purpose. Phylogenetic analyses suggested that Archaeal inulosucrases have been acquired from halophilic bacilli through horizontal gene transfer, with a HX(H/F)T motif evolving further into a HXHT motif, together with a unique D residue creating the onset of a specific alternative acceptor binding groove. This work uncovers a novel area in fructan research, highlighting unexplored aspects of life in hypersaline habitats, and raising questions about the general physiological relevance of inulosucrases and their products in nature.

Metagenomic insights into the metabolism and evolution of a new Thermoplasmata order (Candidatus Gimiplasmatales)

Thermoplasmata is a widely distributed and ecologically important archaeal class in the phylum Euryarchaeota. Because few cultures and genomes are available, uncharacterized Thermoplasmata metabolisms remain unexplored. In this study, we obtained four medium- to high-quality archaeal metagenome-assembled genomes (MAGs) from the filamentous fragments of black-odorous aquatic sediments (Foshan, Guangdong, China). Based on their 16S rRNA gene and ribosomal protein phylogenies, the four MAGs belong to the previously unnamed Thermoplasmata UBA10834 clade. We propose that this clade (five reference genomes from the Genome Taxonomy Database (GTDB) and four MAGs from this study) be considered a new order, Candidatus Gimiplasmatales. Metabolic pathway reconstructions indicated that the Ca. Gimiplasmatales MAGs can biosynthesize isoprenoids and nucleotides de novo. Additionally, some taxa have genes for formaldehyde and acetate assimilation, and the Wood-Ljungdahl CO₂ -fixation pathway, indicating a mixotrophic lifestyle. Sulfur reduction, hydrogen metabolism, and arsenic detoxification pathways were predicted, indicating sulfur-, hydrogen-, and arsenic-transformation potentials. Comparative genomics indicated that the H₄ F Wood-Ljungdahl pathway of both Ca. Gimiplasmatales and Methanomassiliicoccales was likely obtained by the interdomain lateral gene transfer from the Firmicutes. Collectively, this study elucidates the taxonomic and potential metabolic diversity of the new order Ca. Gimiplasmatales and the evolution of this subgroup and its sister lineage Methanomassiliicoccales.

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.

Genomic and transcriptomic insights into methanogenesis potential of novel methanogens from mangrove sediments

BACKGROUND

Methanogens are crucial to global methane budget and carbon cycling. Methanogens from the phylum Euryarchaeota are currently classified into one class and seven orders, including two novel methanogen taxa, Methanofastidiosa and Methanomassiliicoccales. The relative importance of the novel methanogens to methane production in the natural environment is poorly understood.

RESULTS

Here, we used a combined metagenomic and metatranscriptomic approach to investigate the metabolic activity of methanogens in mangrove sediments in Futian Nature Reserve, Shenzhen. We obtained 13 metagenome-assembled genomes (MAGs) representing one class (Methanofastidiosa) and five orders (Methanomassiliicoccales, Methanomicrobiales, Methanobacteriales, Methanocellales, and Methanosarcinales) of methanogens, including the two novel methanogens. Comprehensive annotation indicated the presence of an H₂-dependent methylotrophic methanogenesis pathway in Methanofastidiosa and Methanomassiliicoccales. Based on the functional gene analysis, hydrogenotrophic and methylotrophic methanogenesis are the dominant pathways in mangrove sediments. MAG mapping revealed that hydrogenotrophic Methanomicrobiales were the most abundant methanogens and that methylotrophic Methanomassiliicoccales were the most active methanogens in the analyzed sediment profile, suggesting their important roles in methane production.

CONCLUSIONS

Partial or near-complete genomes of two novel methanogen taxa, Methanofastidiosa and Methanomassiliicoccales, in natural environments were recovered and analyzed here for the first time. The presented findings highlight the ecological importance of the two novel methanogens and complement knowledge of how methane is produced in mangrove ecosystem. This study implies that two novel methanogens play a vital role in carbon cycle. Video Abstract.

Current Status and Potential Applications of Underexplored Prokaryotes

Thousands of prokaryotic genera have been published, but methodological bias in the study of prokaryotes is noted. Prokaryotes that are relatively easy to isolate have been well-studied from multiple aspects. Massive quantities of experimental findings and knowledge generated from the well-known prokaryotic strains are inundating scientific publications. However, researchers may neglect or pay little attention to the uncommon prokaryotes and hard-to-cultivate microorganisms. In this review, we provide a systematic update on the discovery of underexplored culturable and unculturable prokaryotes and discuss the insights accumulated from various research efforts. Examining these neglected prokaryotes may elucidate their novelties and functions and pave the way for their industrial applications. In addition, we hope that this review will prompt the scientific community to reconsider these untapped pragmatic resources.