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Whole microbial communities regularly merge with one another, often in tandem with their environments, in a process called community coalescence. Such events impose substantial changes: abiotic perturbation from environmental blending and biotic perturbation of community merging. We used an aquatic mixing experiment to unravel the effects of these perturbations on the whole microbiome response and on the success of individual taxa when distinct freshwater and marine communities coalesce. We found that an equal mix of freshwater and marine habitats and blended microbiomes resulted in strong convergence of the community structure toward that of the marine microbiome. The enzymatic potential of these blended microbiomes in mixed media also converged toward that of the marine, with strong correlations between the multivariate response patterns of the enzymes and of community structure. Exposing each endmember inocula to an axenic equal mix of their freshwater and marine source waters led to a 96% loss of taxa from our freshwater microbiomes and a 66% loss from our marine microbiomes. When both inocula were added together to this mixed environment, interactions amongst the communities led to a further loss of 29% and 49% of freshwater and marine taxa, respectively. Under both the axenic and competitive scenarios, the diversity lost was somewhat counterbalanced by increased abundance of microbial taxa that were too rare to detect in the initial inocula. Our study emphasizes the importance of the rare biosphere as a critical component of microbial community responses to community coalescence. [ABSTRACT FROM AUTHOR]

We performed an incubation experiment of seawater confined in plastic bottles with samples collected at three depths (15, 60, and 90 m) after retrieval from a single offshore location in the Mediterranean Sea, from a late summer stratified water column. Two samples representative of each depth were collected and stored in opaque bottles after two periods of 7 h. We took advantage of the “bottle effect” to investigate changes in the natural microbial communities (abundant and rare). We recovered 94 metagenome-assembled genomes (MAGs) and 1089 metagenomic viral contigs and examined their abundance using metagenomic recruitment. We detected a significant fast growth of copiotrophic bacteria such as Alteromonas or Erythrobacter throughout the entire water column with different dynamics that we assign to “clonal,” “polyclonal,” or “multispecies” depending on the recruitment pattern. Results also showed a marked ecotype succession in the phototropic picocyanobacteria that were able to grow at all the depths in the absence of light, highlighting the importance of their mixotrophic potential. In addition, “wall-chain-reaction” hypothesis based on the study of phage–host dynamics showed the higher impact of viral predation on archaea in deeper waters, evidencing their prominent role during incubations. Our results provide a step forward in understanding the mechanisms underlying dynamic patterns and ecology of the marine microbiome and the importance of processing the samples immediately after collection to avoid changes in the community structure.

Wildfires destabilize biocrust, requiring decades for most biological constituents to regenerate, but bacteria may recover quickly and mitigate the detrimental consequences of burnt soils. To evaluate the short-term recovery of biocrust bacteria, we tracked shifts in bacterial community form and function in Cyanobacteria/lichen-dominated (shrub interspaces) and Cyanobacteria/moss-dominated (beneath Artemisia tridentata) biocrusts 1 week, 2 months, and 1 year following a large-scale burn manipulations in a cold desert (Utah, USA). We found no evidence of the burned bacterial community recovering to a burgeoning biocrust. The foundational biocrust phyla, Cyanobacteria, dominated by Microcoleus viginatus (Microcoleaceae), disappeared from burned soils creating communities void of photosynthetic taxa. One year after the fire, the burned biocrust constituents had eroded away and the bare soils supported the formation of a convergent community of chemoheterotrophic copiotrophs regardless of location. The emergent community was dominated by a previously rare Planococcus species (family Planococcaceae, Firmicutes) and taxa in the Cellulomonadaceae (Actinobacteria), and Oxalobacteraceae (Betaproteobacteria). Previously burnt soils maintained similar levels of bacterial biomass, alpha diversity, and richness as unburned biocrusts, but supported diffuse, poorly-interconnected communities with 75% fewer species interactions. Nitrogen fixation declined at least 3.5-fold in the burnt soils but ammonium concentrations continued to rise through the year, suggesting that the exhaustion of organic C released from the fire, and not N, may diminish the longevity of the emergent community. Our results demonstrate that biocrust bacteria may recover rapidly after burning, albeit along a different community trajectory, as rare bacteria become dominant, species interconnectedness diminishes, and ecosystem services fail to rebound.

Community assembly processes are complex and understanding them represents a challenge in microbial ecology. Here, we used Lascaux Cave as a stable, confined environment to quantify the importance of stochastic vs deterministic processes during microbial community dynamics across the three domains of life in relation to an anthropogenic disturbance that had resulted in the side-by-side occurrence of a resistant community (unstained limestone), an impacted community (present in black stains), and a resilient community (attenuated stains). Metabarcoding data showed that the microbial communities of attenuated stains, black stains, and unstained surfaces differed, with attenuated stains being in an intermediate position. We found four scenarios to explain community response to disturbance in stable conditions for the three domains of life. Specifically, we proposed the existence of a fourth, not-documented yet scenario that concerns the always-rare microbial taxa, where stochastic processes predominate even after disturbance but are replaced by deterministic processes during post-disturbance recovery. This suggests a major role of always-rare taxa in resilience, perhaps because they might provide key functions required for ecosystem recovery.IMPORTANCEThe importance of stochastic vs deterministic processes in cave microbial ecology has been a neglected topic so far, and this work provided an opportunity to do so in a context related to the dynamics of black-stain alterations in Lascaux, a UNESCO Paleolithic cave. Of particular significance was the discovery of a novel scenario for always-rare microbial taxa in relation to disturbance, in which stochastic processes are replaced later by deterministic processes during post-disturbance recovery, i.e., during attenuation of black stains., Competing Interests: The authors declare no conflict of interest.

We performed an incubation experiment of seawater confined in plastic bottles with samples collected at three depths (15, 60, and 90 m) after retrieval from a single offshore location in the Mediterranean Sea, from a late summer stratified water column. Two samples representative of each depth were collected and stored in opaque bottles after two periods of 7 h. We took advantage of the "bottle effect" to investigate changes in the natural microbial communities (abundant and rare). We recovered 94 metagenome-assembled genomes (MAGs) and 1089 metagenomic viral contigs and examined their abundance using metagenomic recruitment. We detected a significant fast growth of copiotrophic bacteria such as Alteromonas or Erythrobacter throughout the entire water column with different dynamics that we assign to "clonal," "polyclonal," or "multispecies" depending on the recruitment pattern. Results also showed a marked ecotype succession in the phototropic picocyanobacteria that were able to grow at all the depths in the absence of light, highlighting the importance of their mixotrophic potential. In addition, "wall-chain-reaction" hypothesis based on the study of phage–host dynamics showed the higher impact of viral predation on archaea in deeper waters, evidencing their prominent role during incubations. Our results provide a step forward in understanding the mechanisms underlying dynamic patterns and ecology of the marine microbiome and the importance of processing the samples immediately after collection to avoid changes in the community structure. [ABSTRACT FROM AUTHOR]

• The relative abundance of soil rare biosphere was stable under climate changes. • The specific soil microbial taxa strongly related to soil rare biosphere. • The rare biosphere strongly explained variations of soil available nitrogen. Ecological roles of "rare biosphere" (RB) were rarely discussed in alpine grassland ecosystems. We explored the roles of RB and specific taxa of soil bacteria and fungi in regulating soil nutrients and aboveground biomass of an alpine meadow and alpine steppe under warming and enhanced rainfall scenarios on the Qinghai-Tibetan plateau. In the context of alpine meadow and alpine steppe, the relative abundance of bacterial RB was ∼40% in the bacterial community, and it was <10% for fungal RB in the fungal community. The relative abundance of the RB of soil bacteria and fungi were not changed by warming or enhanced rainfall. All specific bacterial taxa and over 90% specific fungal taxa belonged to the RB. The RB, including the most specific taxa, explained many more variations in the contents of soil NO 3 -N and NH 4 -N than the high abundant microbial species under warming and enhanced rainfall conditions. The aboveground biomass of the alpine meadow and steppe were strongly affected by the contents of soil NO 3 -N, available phosphorus and total nitrogen under the condition of warming and enhanced rainfall. Our findings suggest that the robust soil microbial RB plays an important role in regulating the content of soil available nitrogen, which could profoundly affect aboveground plant biomass of alpine grassland ecosystems under climate change conditions. [ABSTRACT FROM AUTHOR]

Microbial-driven straw decomposition is important for soil organic carbon accumulation, nutrient uptake, and crop utilization. However, the mechanism by which tillage and fertilization interactions form the abundant and rare microbial communities that mediate straw degradation in dry farmland remains unclear. Based on an interaction experiment between three tillage practices (zero-till, chisel-till, and conventional plow-till) and three levels of nitrogen fertilizer (180, 240, and 300 kg·N·ha−1), we aimed to understand the community assembly process of abundant and rare microbe in the decomposition of maize straw. We found that the abundant bacterial and fungal communities were governed by stochastic processes, whereas the rare bacterial communities were dominated by deterministic processes. Furthermore, the relative importance of deterministic assembly of all microbial communities was higher in conservation tillage; in addition, the deterministic assembly process of the abundant bacterial and fungal communities was significantly increased by the medium level of nitrogen fertilizer (240 kg·N·ha−1), but the rare microbial community was not significantly affected. Redundancy analysis (RDA) and threshold indicator taxa analysis (TITAN) indicated that soil temperature, pH, and NO 3 − are the key influencing factors for the abundant and rare microbial communities. Overall, conservation tillage and a medium level of nitrogen fertilizer (240 kg·ha−1) in dry farmland promoted straw decomposition by regulating the development and turnover of straw-decomposing communities, in which they regulated bacterial community succession rather than fungi within a short decomposition time. These findings highlight the distinct responses to conservation tillage and N fertilization in the community assembly of abundant and rare biospheres in maize straw decomposition, and provide additional evidence for the development of conservation tillage applications in drylands. • The assembly of straw microbial communities was dominated by stochastic process. • Conservation tillage enhanced the contribution of deterministic process. • High nitrogen fertilization leads to the high contribution of stochastic process. • Microbial assembly of maize straw was affected by soil temperature, pH, and NO 3 −. • Abundant bacterial and abundant rare fungal taxa were keystones under conservation tillage. [ABSTRACT FROM AUTHOR]

A substantial portion of global coal seam methane reserves are biogenically produced. To enhance methane production, recent research has focussed on genetic surveying of the microbial life inhabiting these coal seams. These surveys have revealed that the most abundant organisms in these microbial communities are taxa specialised in metabolism of various simple substrates, and are typically methanogens, their (presumably) syntrophic acetate-oxidising bacterial partners, and other bacterial taxa associated with biomass recycling. Although abundant, these microbes are incapable of directly accessing the vast majority of recalcitrant carbon contained within the coal geopolymer. Instead, these more abundant taxa likely rely on the low abundance but diverse taxa, known as the 'rare taxa', to transform the carbon within coal into simpler, more labile substrates. Since these rare taxa typically have low taxonomic resolution, their probable activities within the coal seam environment are difficult to infer using the standard 16S rDNA community surveys. Therefore, the present study aimed to develop a method for identifying and characterising these rare taxa using a metagenomic approach. Using this method, a near-complete genome from a Deltaproteobacteria sp. (CSMB_808; designation taken from the Coal Seam Microbiome reference set) was recovered from a metagenome sampling the Surat Basin, Australia, and comprised only 0.5% of the total 16S rDNA sequences recovered from this metagenome. Genetically, CSMB_808 appears to be a motile fatty acid and possibly alkane-degrader within the coal seam environment, and may play an important role in the coal-to-methane degradative pathways. Despite the near-completeness of the recovered genome, the taxonomic resolution of this deltaproteobacterium was unable to be clarified due to insufficient described close relatives. Together, the low taxonomic resolution, relatively low 16S rDNA abundance, and ability to degrade putative upstream metabolites that may facilitate methanogenesis in the coal seam environment, indicates that this method of analysis can assist in understanding other important but uncharacterised rare taxa of the coal seam microbiome. A clearer understanding of the function of these taxa would allow targeted strategies to enhance methane production, as well as contributing valuable knowledge of carbon cycling in the terrestrial subsurface. [ABSTRACT FROM AUTHOR]

To date, it remains unclear how anthropogenic perturbations influence the dynamics of microbial communities, what general patterns arise in response to disturbance, and whether it is possible to predict them. Here, we suggest the use of microbial mats as a model of study to reveal patterns that can illuminate the ecological processes underlying microbial dynamics in response to stress. We traced the responses to anthropogenic perturbation caused by water depletion in microbial mats from Cuatro Cienegas Basin (CCB), Mexico, by using a time-series spatially resolved analysis in a novel combination of three computational approaches. First, we implemented MEBS (Multi-genomic Entropy-Based Score) to evaluate the dynamics of major biogeochemical cycles across spatio-temporal scales with a single informative value. Second, we used robust Time Series-Ecological Networks (TS-ENs) to evaluate the total percentage of interactions at different taxonomic levels. Lastly, we utilized network motifs to characterize specific interaction patterns. Our results indicate that microbial mats from CCB contain an enormous taxonomic diversity with at least 100 phyla, mainly represented by members of the rare biosphere (RB). Statistical ecological analyses point out a clear involvement of anaerobic guilds related to sulfur and methane cycles during wet versus dry conditions, where we find an increase in fungi, photosynthetic, and halotolerant taxa. TS-ENs indicate that in wet conditions, there was an equilibrium between cooperation and competition (positive and negative relationships, respectively), while under dry conditions there is an over-representation of negative relationships. Furthermore, most of the keystone taxa of the TS-ENs at family level are members of the RB and the microbial mat core highlighting their crucial role within the community. Our results indicate that microbial mats are more robust to perturbation due to redundant functions that are likely shared among community members in the highly connected TS-ENs with density values close to one (≈0.9). Finally, we provide evidence that suggests that a large taxonomic diversity where all community members interact with each other (low modularity), the presence of permanent of low-abundant taxa, and an increase in competition can be potential buffers against environmental disturbance in microbial mats.

ABSTRACT The 2,3-seco pathway, the pathway for anaerobic cholesterol degradation, has been established in the denitrifying betaproteobacterium Sterolibacterium denitrificans. However, knowledge of how microorganisms respond to cholesterol at the community level is elusive. Here, we applied mesocosm incubation and 16S rRNA sequencing to reveal that, in denitrifying sludge communities, three betaproteobacterial operational taxonomic units (OTUs) with low (94% to 95%) 16S rRNA sequence similarity to Stl. denitrificans are cholesterol degraders and members of the rare biosphere. Metatranscriptomic and metabolite analyses show that these degraders adopt the 2,3-seco pathway to sequentially catalyze the side chain and sterane of cholesterol and that two molybdoenzymes—steroid C25 dehydrogenase and 1-testosterone dehydrogenase/hydratase—are crucial for these bioprocesses, respectively. The metatranscriptome further suggests that these betaproteobacterial degraders display chemotaxis and motility toward cholesterol and that FadL-like transporters may be the key components for substrate uptake. Also, these betaproteobacteria are capable of transporting micronutrients and synthesizing cofactors essential for cellular metabolism and cholesterol degradation; however, the required cobalamin is possibly provided by cobalamin-de novo-synthesizing gamma-, delta-, and betaproteobacteria via the salvage pathway. Overall, our results indicate that the ability to degrade cholesterol in sludge communities is reserved for certain rare biosphere members and that C25 dehydrogenase can serve as a biomarker for sterol degradation in anoxic environments. IMPORTANCE Steroids are ubiquitous and abundant natural compounds that display recalcitrance. Biodegradation via sludge communities in wastewater treatment plants is the primary removal process for steroids. To date, compared to studies for aerobic steroid degradation, the knowledge of anaerobic degradation of steroids has been based on only a few model organisms. Due to the increase of anthropogenic impacts, steroid inputs may affect microbial diversity and functioning in ecosystems. Here, we first investigated microbial functional responses to cholesterol, the most abundant steroid in sludge, at the community level. Our metagenomic and metatranscriptomic analyses revealed that the capacities for cholesterol approach, uptake, and degradation are unique traits of certain low-abundance betaproteobacteria, indicating the importance of the rare biosphere in bioremediation. Apparent expression of genes involved in cofactor de novo synthesis and salvage pathways suggests that these micronutrients play important roles for cholesterol degradation in sludge communities.

Little is known about the distribution and ecological functions of abundant, intermediate, and rare biospheres and their correlations with environmental factors in hot springs. Here, we explored the microbial community composition of total, abundant, intermediate, and rare biospheres in 66 Tibetan hot springs (pairwise geographic distance 0–610 km, temperature 32–86°C, pH 3.0–9.5, and salinity 0.13–1.32 g/L) with the use of Illumina MiSeq high-throughput sequencing. The results showed that the abundant sub-communities were mainly composed of Chloroflexi, Proteobacteria, Deinococcus-Thermus, Aquificae, Bacteroidetes, and Firmicutes. In contrast, the rare sub-communities mainly consisted of most newly proposed or candidate phyla of Dictyoglomi, Hydrogenedentes, Atribacteria, Hadesarchaea, Aminicenantes, Microgenomates, Calescamantes, Omnitrophica, Altiarchaeales, and Chlamydiae. However, the abundant and rare sub-communities shared some common phyla (e.g., Crenarchaeota, Bathyarchaeota, and Chlorobi), which were composed of different OTUs. The abundant, intermediate, and rare sub-communities were mainly influenced by different environmental variables, which could be ascribed to the fact that they may have different growth and activity and thus respond differently to these variables. Spatial factors showed more contribution to shaping of the intermediate and rare communities than to abundant sub-community, suggesting that the abundant taxa were more easily dispersed than their rare counterparts among hot springs. Microbial ecological function prediction revealed that the abundant and rare sub-communities responded differently to the measured environmental factors, suggesting they may occupy different ecological niches in hot springs. The rare sub-communities may play more important roles in organic matter degradation than their abundant counterparts in hot springs. Collectively, this study provides a better understanding on the microbial community structure and potential ecological functions of the abundant and rare biospheres in hot spring ecosystems. The identified rare taxa provide new opportunities of ecological, taxonomic and genomic discoveries in Tibetan hot springs.

Cultivation of undescribed rumen microorganisms is one of the most important tasks in rumen microbiology. In this study, we aimed to discover the potential of culturomics for characterizing the rumen microbiome and for identifying factors, specifically sample dilution and media type, which affect microbial richness on agar plates. Our cultivation experiment captured 23% of all operational taxonomic units (OTUs) found in the rumen microbiome in this study. The use of different media increased the number of cultured OTUs by up to 40%. Sample dilution had the strongest effect on increasing richness on the plates, while abundance and phylogeny were the main factors determining cultivability of rumen microbes. Our findings from phylogenetic analysis of cultured OTUs on the lower branches of the phylogenetic tree suggest that multifactorial traits govern cultivability. Interestingly, most of our cultured OTUs belonged to the rare rumen biosphere. These cultured OTUs could not be detected in the rumen microbiome, even when we surveyed it across a 38 rumen microbiome samples. These findings add another unique dimension to the complexity of the rumen microbiome and suggest that a large number of different organisms can be cultured in a single cultivation effort.

Deforestation in the Brazilian Amazon occurs at an alarming rate, which has broad effects on global greenhouse gas emissions, carbon storage, and biogeochemical cycles. In this study, soil metagenomes and metagenome-assembled genomes (MAGs) were analyzed for alterations to microbial community composition, functional groups, and putative physiology as it related to land-use change and tropical soil. A total of 28 MAGs were assembled encompassing 10 phyla, including both dominant and rare biosphere lineages. Amazon Acidobacteria subdivision 3, Melainabacteria, Microgenomates, and Parcubacteria were found exclusively in pasture soil samples, while Candidatus Rokubacteria was predominant in the adjacent rainforest soil. These shifts in relative abundance between land-use types were supported by the different putative physiologies and life strategies employed by the taxa. This research provides unique biological insights into candidate phyla in tropical soil and how deforestation may impact the carbon cycle and affect climate change.

The rare biosphere is predicted to aid in maintaining functional redundancy as well as contributing to community turnover across many environments. Recent developments have partially confirmed these hypotheses, while also giving new insights into dormancy and activity among rare communities. However, less attention has been paid to the rare biosphere in soils. This study provides insight into the rare biosphere’s contribution to soil microbial diversity through the study of 781 soil samples representing 24 edaphically diverse sites. Results show that Bray–Curtis dissimilarity for time-sensitive conditionally rare taxa (CRT) does not correlate with whole community dissimilarity, while dissimilarity for space-sensitive CRT only weakly correlate with whole community dissimilarity. This adds to current understanding of spatiotemporal filtering of rare taxa, showing that CRT do not account for community variance across tested soils, but are under the same selective pressure as the whole community.

Archaea are well-recognized components of the human microbiome. However, they appear to be drastically underrepresented compared to the high diversity of bacterial taxa which can be found on various human anatomic sites, such as the gastrointestinal environment, the oral cavity and the skin. As our “microbial” view of the human body, including the methodological concepts used to describe them, has been traditionally biased on bacteria, the question arises whether our current knowledge reflects the actual ratio of archaea versus bacteria or whether we have failed so far to unravel the full diversity of human-associated archaea. This review article hypothesizes that distinct archaeal lineages within humans exist, which still await our detection. First, previously unrecognized taxa might be quite common but they have eluded conventional detection methods. Two recent prime examples are described that demonstrate that this might be the case for specific archaeal lineages. Second, some archaeal taxa might be overlooked because they are rare and/or in low abundance. Evidence for this exists for a broad range of phylogenetic lineages, however we currently do not know whether these sporadically appearing organisms are mere transients or important members of the so called “rare biosphere” with probably basic ecosystem functions. Lastly, evidence exists that different human populations harbor different archaeal taxa and/or the abundance and activity of shared archaeal taxa may differ and thus their impact on the overall microbiome. This research line is rather unexplored and warrants further investigation. While not recapitulating exhaustively all studies on archaeal diversity in humans, this review highlights pertinent recent findings that show that the choice of appropriate methodological approaches and the consideration of different human populations may lead to the detection of archaeal lineages previously not associated with humans. This in turn will help understand variations found in the overall microbiomes from different individuals and ultimately may lead to the emergence of novel concepts/mechanisms impacting human health.

To date, it remains unclear how anthropogenic perturbations influence the dynamics of microbial communities, what general patterns arise in response to disturbance, and whether it is possible to predict them. Here, we suggest the use of microbial mats as a model of study to reveal patterns that can illuminate the ecological processes underlying microbial dynamics in response to stress. We traced the responses to anthropogenic perturbation caused by water depletion in microbial mats from Cuatro Cienegas Basin (CCB), Mexico, by using a time-series spatially resolved analysis in a novel combination of three computational approaches. First, we implemented MEBS (Multi-genomic Entropy-Based Score) to evaluate the dynamics of major biogeochemical cycles across spatio-temporal scales with a single informative value. Second, we used robust Time Series-Ecological Networks (TS-ENs) to evaluate the total percentage of interactions at different taxonomic levels. Lastly, we utilized network motifs to characterize specific interaction patterns. Our results indicate that microbial mats from CCB contain an enormous taxonomic diversity with at least 100 phyla, mainly represented by members of the rare biosphere (RB). Statistical ecological analyses point out a clear involvement of anaerobic guilds related to sulfur and methane cycles during wet versus dry conditions, where we find an increase in fungi, photosynthetic, and halotolerant taxa. TS-ENs indicate that in wet conditions, there was an equilibrium between cooperation and competition (positive and negative relationships, respectively), while under dry conditions there is an over-representation of negative relationships. Furthermore, most of the keystone taxa of the TS-ENs at family level are members of the RB and the microbial mat core highlighting their crucial role within the community. Our results indicate that microbial mats are more robust to perturbation due to redundant functions that are likely shared among community members in the highly connected TS-ENs with density values close to one (≈0.9). Finally, we provide evidence that suggests that a large taxonomic diversity where all community members interact with each other (low modularity), the presence of permanent of low-abundant taxa, and an increase in competition can be potential buffers against environmental disturbance in microbial mats. [ABSTRACT FROM AUTHOR]

Little is known about the distribution and ecological functions of abundant, intermediate, and rare biospheres and their correlations with environmental factors in hot springs. Here, we explored the microbial community composition of total, abundant, intermediate, and rare biospheres in 66 Tibetan hot springs (pairwise geographic distance 0–610 km, temperature 32–86°C, pH 3.0–9.5, and salinity 0.13–1.32 g/L) with the use of Illumina MiSeq high-throughput sequencing. The results showed that the abundant sub-communities were mainly composed of Chloroflexi, Proteobacteria, Deinococcus-Thermus, Aquificae, Bacteroidetes , and Firmicutes. In contrast, the rare sub-communities mainly consisted of most newly proposed or candidate phyla of Dictyoglomi, Hydrogenedentes, Atribacteria, Hadesarchaea, Aminicenantes, Microgenomates, Calescamantes, Omnitrophica, Altiarchaeales , and Chlamydiae. However, the abundant and rare sub-communities shared some common phyla (e.g., Crenarchaeota, Bathyarchaeota , and Chlorobi), which were composed of different OTUs. The abundant, intermediate, and rare sub-communities were mainly influenced by different environmental variables, which could be ascribed to the fact that they may have different growth and activity and thus respond differently to these variables. Spatial factors showed more contribution to shaping of the intermediate and rare communities than to abundant sub-community, suggesting that the abundant taxa were more easily dispersed than their rare counterparts among hot springs. Microbial ecological function prediction revealed that the abundant and rare sub-communities responded differently to the measured environmental factors, suggesting they may occupy different ecological niches in hot springs. The rare sub-communities may play more important roles in organic matter degradation than their abundant counterparts in hot springs. Collectively, this study provides a better understanding on the microbial community structure and potential ecological functions of the abundant and rare biospheres in hot spring ecosystems. The identified rare taxa provide new opportunities of ecological, taxonomic and genomic discoveries in Tibetan hot springs. [ABSTRACT FROM AUTHOR]

Cultivation of undescribed rumen microorganisms is one of the most important tasks in rumen microbiology. In this study, we aimed to discover the potential of culturomics for characterizing the rumen microbiome and for identifying factors, specifically sample dilution and media type, which affect microbial richness on agar plates. Our cultivation experiment captured 23% of all operational taxonomic units (OTUs) found in the rumen microbiome in this study. The use of different media increased the number of cultured OTUs by up to 40%. Sample dilution had the strongest effect on increasing richness on the plates, while abundance and phylogeny were the main factors determining cultivability of rumen microbes. Our findings from phylogenetic analysis of cultured OTUs on the lower branches of the phylogenetic tree suggest that multifactorial traits govern cultivability. Interestingly, most of our cultured OTUs belonged to the rare rumen biosphere. These cultured OTUs could not be detected in the rumen microbiome, even when we surveyed it across a 38 rumen microbiome samples. These findings add another unique dimension to the complexity of the rumen microbiome and suggest that a large number of different organisms can be cultured in a single cultivation effort. [ABSTRACT FROM AUTHOR]

Abstract: The description of a rare biosphere within microbial communities has created great interest because microbes play a fundamental role in the functioning of all ecosystems on earth. Despite recent progress in understanding the ecology of the rare biosphere, the concept itself is still discussed, and fundamental questions remain. Here, we target the seed bank compartment of the rare biosphere, assess the level of rarity at which micro‐organisms are still able to colonize an ecosystem and investigate whether rare species are functionally redundant. Using an original experimental design where wood in aquaria was inoculated with increasingly diluted coastal seawater, we show that bacteria that represented as few as 0.00000002% of the cells in the environment (or 1 cell in 10 L of seawater) were still able to grow and play key roles within the ecosystem. Our experiment further showed that some bacteria can be replaced by others that have the potential to fulfil the same metabolic tasks. This finding suggests some functional redundancy within bacterial species. However, when ultrarare bacteria were progressively removed, productivity was reduced, and below a certain threshold some processes were lost, and the function of the ecosystem was altered. Overall the study shows that bacteria that are not detected by high‐throughput sequencing approaches are nevertheless viable and able to colonize new ecosystems, suggesting the need to consider ultrarare microbes in the marine environment. [ABSTRACT FROM AUTHOR]

Recent analyses revealed that most of the biodiversity observed in marine microbial communities is represented by organisms with low abundance but, nonetheless essential for ecosystem dynamics and processes across both temporal and spatial scales. Surprisingly, few studies have considered the effect of macroorganism–microbe interactions on the ecology and distribution dynamics of rare microbial taxa. In this review, we synthesize several lines of evidence that these relationships cannot be neglected any longer. First, we provide empirical support that the microbiota of macroorganisms represents a significant part of marine bacterial biodiversity and that host-microbe interactions benefit to certain microbial populations which are part of the rare biosphere (i.e., opportunistic copiotrophic organisms). Second, we reveal the major role that macroorganisms may have on the dispersal and the geographic distribution of microbes. Third, we introduce an innovative and integrated view of the interactions between microbes and macroorganisms, namely sustaining the rares, which suggests that macroorganisms favor the maintenance of marine microbial diversity and are involved in the regulation of its richness and dynamics. Finally, we show how this hypothesis complements existing theories in microbial ecology and offers new perspectives about the importance of macroorganisms for the microbial biosphere, particularly the rare members.

Plant growth can be affected by soil bacteria. In turn, plants are known to influence soil bacteria through rhizodeposits and changes in abiotic conditions. We aimed to quantify the phylotype richness and relative abundance of rhizosphere bacteria that are actually influenced in a plant species-specific manner and to determine the role of the disproportionately large diversity of low-abundance bacteria belonging to the rare biosphere (

The rare biosphere, the low abundant microbial populations, is suggested to be a conserved way of microbial life. Here we conducted a molecular survey of rare methanogenic archaea in the environment targeting the mcrA gene in order to test if general concepts associated with the structure of the rare bacterial biosphere also apply to single functional groups. Similar to what is known about rare bacterial communities, the contribution of rare methanogens to the alpha diversity is much larger than to Bray-Curtis measures. Moreover, a similar core group of methanogens harbored by the abundant and rare communities suggests similar sources and environmental controls of both groups. Among the communities of different levels of rarity, the conditionally rare methanogenic taxa largely account for the overall community dynamics of the rare biosphere and likely enter the dominant community under favorable environmental conditions. In addition, we observed a positive correlation between the alpha diversity and the production of methane when the rare taxa were taken into account. This supports the concept that increasing microbial biodiversity enhances ecological function. The composition and environmental associations of the rare methanogenic biosphere allow us to conclude that rarity is a conserved way also for single functional groups. [ABSTRACT FROM AUTHOR]

Recent analyses revealed that most of the biodiversity observed in marine microbial communities is represented by organisms with low abundance but, nonetheless essential for ecosystem dynamics and processes across both temporal and spatial scales. Surprisingly, few studies have considered the effect of macroorganism-microbe interactions on the ecology and distribution dynamics of rare microbial taxa. In this review, we synthesize several lines of evidence that these relationships cannot be neglected any longer. First, we provide empirical support that the microbiota of macroorganisms represents a significant part of marine bacterial biodiversity and that host-microbe interactions benefit to certain microbial populations which are part of the rare biosphere (i.e., opportunistic copiotrophic organisms). Second, we reveal the major role that macroorganisms may have on the dispersal and the geographic distribution of microbes. Third, we introduce an innovative and integrated view of the interactions between microbes and macroorganisms, namely sustaining the rares, which suggests that macroorganisms favor the maintenance of marine microbial diversity and are involved in the regulation of its richness and dynamics. Finally, we show how this hypothesis complements existing theories in microbial ecology and offers new perspectives about the importance of macroorganisms for the microbial biosphere, particularly the rare members. [ABSTRACT FROM AUTHOR]

One of the major contemporary challenges in microbial ecology has been to discriminate the reactive core from the random, unreactive components of bacterial communities. In previous work we used the spatial abundance distributions of bacterioplankton across boreal lakes of Québec to group taxa into four distinct categories that reflect either hydrology-mediated dispersal along the aquatic network or environmental selection mechanisms within lakes. Here, we test whether this categorization derived from the spatial distribution of taxa is maintained over time, by analyzing the temporal dynamics of the operational taxonomic units (OTUs) within those spatially derived categories along an annual cycle in the oligotrophic lake Croche (Québec, Canada), and assessing the coherence in the patterns of abundance, occurrence, and environmental range of these OTUs over space and time. We report that the temporal dynamics of most taxa within a single lake are largely coherent with those derived from their spatial distribution over large spatial scales, suggesting that these properties must be intrinsic of particular taxa. We also identified a set of rare taxa cataloged as having a random occupancy based on their spatial distribution, but which showed clear seasonality and abundance peaks along the year, yet these comprised a very small fraction of the total rare OTUs. We conclude that the presence of most rare bacterioplankton taxa in boreal lakes is random, since both their temporal and spatial dynamics suggest links to passive downstream transport and persistence in freshwater networks, rather than environmental selection. [ABSTRACT FROM AUTHOR]

A single liter of water contains hundreds, if not thousands, of bacterial and archaeal species, each of which typically makes up a very small fraction of the total microbial community (<0.1%), the so-called "rare biosphere." How often, and via what mechanisms, e.g., clonal amplification versus horizontal gene transfer, the rare taxa and genes contribute to microbial community response to environmental perturbations represent important unanswered questions toward better understanding the value and modeling of microbial diversity. We tested whether rare species frequently responded to changing environmental conditions by establishing 20-liter planktonic mesocosms with water from Lake Lanier (Georgia, USA) and perturbing them with organic compounds that are rarely detected in the lake, including 2,4-dichlorophenoxyacetic acid (2,4-D), 4-nitrophenol (4-NP), and caffeine. The populations of the degraders of these compounds were initially below the detection limit of quantitative PCR (qPCR) or metagenomic sequencing methods, but they increased substantially in abundance after perturbation. Sequencing of several degraders (isolates) and time-series metagenomic data sets revealed distinct cooccurring alleles of degradation genes, frequently carried on transmissible plasmids, especially for the 2,4-D mesocosms, and distinct species dominating the post-enrichment microbial communities from each replicated mesocosm. This diversity of species and genes also underlies distinct degradation profiles among replicated mesocosms. Collectively, these results supported the hypothesis that the rare biosphere can serve as a genetic reservoir, which can be frequently missed by metagenomics but enables community response to changing environmental conditions caused by organic pollutants, and they provided insights into the size of the pool of rare genes and species. IMPORTANCE: A single liter of water or gram of soil contains hundreds of lowabundance bacterial and archaeal species, the so called rare biosphere. The value of this astonishing biodiversity for ecosystem functioning remains poorly understood, primarily due to the fact that microbial community analysis frequently focuses on abundant organisms. Using a combination of culture-dependent and culture-independent (metagenomics) techniques, we showed that rare taxa and genes commonly contribute to the microbial community response to organic pollutants. Our findings should have implications for future studies that aim to study the role of rare species in environmental processes, including environmental bioremediation efforts of oil spills or other contaminants. [ABSTRACT FROM AUTHOR]

Strain LMG 31809 T was isolated from a top soil sample of a temperate, mixed deciduous forest in Belgium. Comparison of its 16S rRNA gene sequence with that of type strains of bacteria with validly published names positioned it in the class Alphaproteobacteria and highlighted a major evolutionary divergence from its near neighbor species which represented species of the orders Emcibacterales and Sphingomonadales. 16S rRNA amplicon sequencing of the same soil sample revealed a highly diverse community in which Acidobacteria and Alphaproteobacteria predominated, but failed to yield amplicon sequence variants highly similar to that of strain LMG 31809 T. There were no metagenome assembled genomes that corresponded to the same species and a comprehensive analysis of public 16S rRNA amplicon sequencing data sets demonstrated that strain LMG 31809 T represents a rare biosphere bacterium that occurs at very low abundances in multiple soil and water-related ecosystems. The genome analysis suggested that this strain is a strictly aerobic heterotroph that is asaccharolytic and uses organic acids and possibly aromatic compounds as growth substrates. We propose to classify LMG 31809 T as a novel species within a novel genus, Govania unica gen. nov., sp. nov, within the novel family Govaniaceae of the class Alphaproteobacteria. Its type strain is LMG 31809 T (=CECT 30155 T). The whole-genome sequence of strain LMG 31809 T has a size of 3.21 Mbp. The G + C content is 58.99 mol%. The 16S rRNA gene and whole-genome sequences of strain LMG 31809 T are publicly available under accession numbers OQ161091 and JANWOI000000000, respectively. [ABSTRACT FROM AUTHOR]

ABSTRACT High-throughput sequencing of small-subunit (SSU) rRNA genes has revolutionized understanding of microbial communities and facilitated investigations into ecological dynamics at unprecedented scales. Such extensive SSU rRNA gene sequence libraries, constructed from DNA extracts of environmental or host-associated samples, often contain a substantial proportion of unclassified sequences, many representing organisms with novel taxonomy (taxonomic “blind spots”) and potentially unique ecology. Indeed, these novel taxonomic lineages are associated with so-called microbial “dark matter,” which is the genomic potential of these lineages. Unfortunately, characterization beyond “unclassified” is challenging due to relatively short read lengths and large data set sizes. Here we demonstrate how mining of phylogenetically novel sequences from microbial ecosystems can be automated using SSUnique, a software pipeline that filters unclassified and/or rare operational taxonomic units (OTUs) from 16S rRNA gene sequence libraries by screening against consensus structural models for SSU rRNA. Phylogenetic position is inferred against a reference data set, and additional characterization of novel clades is also included, such as targeted probe/primer design and mining of assembled metagenomes for genomic context. We show how SSUnique reproduced a previous analysis of phylogenetic novelty from an Arctic tundra soil and demonstrate the recovery of highly novel clades from data sets associated with both the Earth Microbiome Project (EMP) and Human Microbiome Project (HMP). We anticipate that SSUnique will add to the expanding computational toolbox supporting high-throughput sequencing approaches for the study of microbial ecology and phylogeny. IMPORTANCE Extensive SSU rRNA gene sequence libraries, constructed from DNA extracts of environmental or host-associated samples, often contain many unclassified sequences, many representing organisms with novel taxonomy (taxonomic “blind spots”) and potentially unique ecology. This novelty is poorly explored in standard workflows, which narrows the breadth and discovery potential of such studies. Here we present the SSUnique analysis pipeline, which will promote the exploration of unclassified diversity in microbiome research and, importantly, enable the discovery of substantial novel taxonomic lineages through the analysis of a large variety of existing data sets.

The ability of ecosystems to adapt to environmental perturbations depends on the duration and intensity of change and the overall biological diversity of the system. While studies have indicated that rare microbial taxa may provide a biological reservoir that supports long-term ecosystem stability, how this dynamic population is influenced by environmental parameters remains unclear. In this study, a microbial mat ecosystem located on San Salvador Island, The Bahamas was used as a model to examine how environmental disturbance affects the protein synthesis potential (PSP) of rare and abundant archaeal and bacterial communities and how these changes impact potential biogeochemical processes. This ecosystem experienced a large shift in salinity (230 to 65 g kg-1) during 2011-2012 following the landfall of Hurricane Irene on San Salvador Island. High throughput sequencing and analysis of 16S rRNA and rRNA genes from samples before and after the pulse disturbance showed significant changes in the diversity and PSP of abundant and rare taxa, suggesting overall compositional and functional sensitivity to environmental change. In both archaeal and bacterial communities, while the majority of taxa showed low PSP across conditions, the overall community PSP increased post-disturbance, with significant shifts occurring among abundant and rare taxa across and within phyla. Broadly, following the post-disturbance reduction in salinity, taxa within Halobacteria decreased while those within Crenarchaeota, Thaumarchaeota, Thermoplasmata, Cyanobacteria, and Proteobacteria, increased in abundance and PSP. Quantitative PCR of genes and transcripts involved in nitrogen and sulfur cycling showed concomitant shifts in biogeochemical cycling potential. Post-disturbance conditions increased the expression of genes involved in N-fixation, nitrification, denitrification, and sulfate reduction. Together, our findings show complex community adaptation to environmental change and help elucidate factors connecting disturbance, biodiversity, and ecosystem function that may enhance ecosystem models.

Land use intensification is associated with loss of biodiversity and altered ecosystem functioning. Until now most studies on the relationship between biodiversity and ecosystem functioning focused on random loss of species, while loss of rare species that usually are the first to disappear received less attention. Here we test if the effect of rare microbial species loss on plant productivity depends on the origin of the microbial soil community. Soils were sampled from three land use types at two farms. Microbial communities with increasing loss of rare species were created by inoculating sterilized soils with serially diluted soil suspensions. After 8 months of incubation, the effects of the different soil communities on abiotic soil properties, soil processes, microbial community composition and plant productivity was measured. Dilution treatments resulted in increasing species loss, which was in relation to abundance of bacteria in the original field soil, without affecting most of the other soil parameters and processes. Microbial species loss affected plant biomass positively, negatively or not at all, depending on soil origin, but not on land use history. Even within fields the effects of dilution on plant biomass varied between replicates, suggesting heterogeneity in microbial community composition. The effects of medium and severe species loss on plant biomass were similar, pointing towards a saturating effect of species loss. We conclude that changes in the composition of the soil microbial community, including rare species loss, can affect plant productivity, depending on the composition of the initial microbial community. Future work on the relation between function and species loss effects should address this variation by including multiple sampling origins.

Aquatic bacterial communities harbour thousands of coexisting taxa. To meet the challenge of discriminating between a 'core' and a sporadically occurring 'random' component of these communities, we explored the spatial abundance distribution of individual bacterioplankton taxa across 198 boreal lakes and their associated fluvial networks (188 rivers). We found that all taxa could be grouped into four distinct categories based on model statistical distributions (normal like, bimodal, logistic and lognormal). The distribution patterns across lakes and their associated river networks showed that lake communities are composed of a core of taxa whose distribution appears to be linked to in-lake environmental sorting (normal-like and bimodal categories), and a large fraction of mostly rare bacteria (94% of all taxa) whose presence appears to be largely random and linked to downstream transport in aquatic networks (logistic and lognormal categories). These rare taxa are thus likely to reflect species sorting at upstream locations, providing a perspective of the conditions prevailing in entire aquatic networks rather than only in lakes. [ABSTRACT FROM AUTHOR]

The ability of ecosystems to adapt to environmental perturbations depends on the duration and intensity of change and the overall biological diversity of the system. While studies have indicated that rare microbial taxa may provide a biological reservoir that supports long-term ecosystem stability, how this dynamic population is influenced by environmental parameters remains unclear. In this study, a microbial mat ecosystem located on San Salvador Island, The Bahamas was used as a model to examine how environmental disturbance affects the protein synthesis potential (PSP) of rare and abundant archaeal and bacterial communities and how these changes impact potential biogeochemical processes. This ecosystem experienced a large shift in salinity (230 to 65 g kg-1) during 2011-2012 following the landfall of Hurricane Irene on San Salvador Island. High throughput sequencing and analysis of 16S rRNA and rRNA genes from samples before and after the pulse disturbance showed significant changes in the diversity and PSP of abundant and rare taxa, suggesting overall compositional and functional sensitivity to environmental change. In both archaeal and bacterial communities, while the majority of taxa showed low PSP across conditions, the overall community PSP increased post-disturbance, with significant shifts occurring among abundant and rare taxa across and within phyla. Broadly, following the post-disturbance reduction in salinity, taxa within Halobacteria decreased while those within Crenarchaeota, Thaumarchaeota, Thermoplasmata, Cyanobacteria, and Proteobacteria, increased in abundance and PSP. Quantitative PCR of genes and transcripts involved in nitrogen and sulfur cycling showed concomitant shifts in biogeochemical cycling potential. Post-disturbance conditions increased the expression of genes involved in N-fixation, nitrification, denitrification, and sulfate reduction. Together, our findings show complex community adaptation to environmental change and help elucidate factors connecting disturbance, biodiversity, and ecosystem function that may enhance ecosystem models. [ABSTRACT FROM AUTHOR]

Bacteria are essential for many ecosystem services but our understanding of factors controlling their functioning is incomplete. While biodiversity has been identified as an important driver of ecosystem processes in macrobiotic communities, we know much less about bacterial communities. Due to the high diversity of bacterial communities, high functional redundancy is commonly proposed as explanation for a lack of clear effects of diversity. The generality of this claim has, however, been questioned. We present the results of an outdoor dilution-to-extinction experiment with four lake bacterial communities. The consequences of changes in bacterial diversity in terms of effective number of species, phylogenetic diversity, and functional diversity were studied for (1) bacterial abundance, (2) temporal stability of abundance, (3) nitrogen concentration, and (4) multifunctionality. We observed a richness gradient ranging from 15 to 280 operational taxonomic units (OTUs). Individual relationships between diversity and functioning ranged from negative to positive depending on lake, diversity dimension, and aspect of functioning. Only between phylogenetic diversity and abundance did we find a statistically consistent positive relationship across lakes. A literature review of 24 peer-reviewed studies that used dilution-to-extinction to manipulate bacterial diversity corroborated our findings: about 25% found positive relationships. Combined, these results suggest that bacteria-driven community functioning is relatively resistant to reductions in diversity. [ABSTRACT FROM AUTHOR]

Scaling laws underpin unifying theories of biodiversity and are among the most predictively powerful relationships in biology. However, scaling laws developed for plants and animals often go untested or fail to hold for microorganisms. As a result, it is unclear whether scaling laws of biodiversity will span evolutionarily distant domains of life that encompass all modes of metabolism and scales of abundance. Using a global-scale compilation of ~35,000 sites and ~5.6.106 species, including the largest ever inventory of high-throughput molecular data and one of the largest compilations of plant and animal community data, we show similar rates of scaling in commonness and rarity across microorganisms and macroscopic plants and animals. We document a universal dominance scaling law that holds across 30 orders of magnitude, an unprecedented expanse that predicts the abundance of dominant ocean bacteria. In combining this scaling law with the lognormal model of biodiversity, we predict that Earth is home to upward of 1 trillion (1012)microbial species. Microbial biodiversity seems greater than ever anticipated yet predictable from the smallest to the largest microbiome. [ABSTRACT FROM AUTHOR]

Little is known about the potential activity of microbial communities in hypersaline sediment ecosystems. Ribosomal tag libraries of DNA and RNA extracted from the sediment of Lake Strawbridge (Western Australia) revealed bacterial and archaeal operational taxonomic units (OTUs) with high RNA/DNA ratios providing evidence for the presence of ‘rare’ but potentially “active” taxa. Among the ‘rare’ bacterial taxaHalomonas, SalinivibrioandIdiomarinashowed the highest protein synthesis potential. Rare but ‘active’ archaeal OTUs were related to the KTK 4A cluster and the Marine-Benthic-Groups B and D. We present the first molecular analysis of the microbial diversity and protein synthesis potential of rare microbial taxa in a hypersaline sediment ecosystem. [ABSTRACT FROM PUBLISHER]