Depth distributions of nitrite reductase (nirK) gene variants reveal spatial dynamics of thaumarchaeal ecotype populations in coastal Monterey Bay

Discordant patterns between nitrogen-cycling functional traits and taxa in distant coastal sediments reveal important community assembly mechanisms

A central question in microbial ecology is how immense microbes are assembled in changing natural environments while executing critical ecosystem functions. Over the past decade, effort has been made to unravel the contribution of stochasticity and determinism to the compositional of microbial communities. However, most studies focus on microbial taxa, ignoring the importance of functional traits. By employing shotgun metagenomic sequencing and state-of-the-art bioinformatics approaches, this study comprehensively investigated the microbially mediated nitrogen (N) cycling processes in two geographically distant coastal locations. Both shotgun and 16S rRNA gene amplicon sequencing demonstrated significantly differed taxonomic compositions between the two sites. The relative abundance of major microbial phyla, such as Pseudomonadota, Thaumarchaeota, and Bacteroidota, significantly differed. In contrast, high homogeneity was observed for N-cycling functional traits. Statistical analyses suggested that N-cycling taxonomic groups were more related to geographic distance, whereas microbial functional traits were more influenced by environmental factors. Multiple community assembly models demonstrated that determinism strongly governed the microbial N-cycling functional traits, whereas their carrying taxonomic groups were highly stochastic. Such discordant patterns between N-cycling functional traits and taxa demonstrated an important mechanism in microbial ecology in which essential ecosystem functions are stably maintained despite geographic distance and stochastic community assembly.

Rhizosphere and detritusphere habitats modulate expression of soil N-cycling genes during plant development

IMPORTANCE

Plant roots modulate microbial nitrogen (N) cycling by regulating the supply of root-derived carbon and nitrogen uptake. These differences in resource availability cause distinct micro-habitats to develop: soil near living roots, decaying roots, near both, or outside the direct influence of roots. While many environmental factors and genes control the microbial processes involved in the nitrogen cycle, most research has focused on single genes and pathways, neglecting the interactive effects these pathways have on each other. The processes controlled by these pathways determine consumption and production of N by soil microorganisms. We followed the expression of N-cycling genes in four soil microhabitats over a period of active root growth for an annual grass. We found that the presence of root litter and living roots significantly altered gene expression involved in multiple nitrogen pathways, as well as tradeoffs between pathways, which ultimately regulate N availability to plants.

Network analysis of 16S rRNA sequences suggests microbial keystone taxa contribute to marine N2O cycling

The mechanisms by which large-scale microbial community function emerges from complex ecological interactions between individual taxa and functional groups remain obscure. We leveraged network analyses of 16S rRNA amplicon sequences obtained over a seven-month timeseries in seasonally anoxic Saanich Inlet (Vancouver Island, Canada) to investigate relationships between microbial community structure and water column N₂O cycling. Taxa separately broadly into three discrete subnetworks with contrasting environmental distributions. Oxycline subnetworks were structured around keystone aerobic heterotrophs that correlated with nitrification rates and N₂O supersaturations, linking N₂O production and accumulation to taxa involved in organic matter remineralization. Keystone taxa implicated in anaerobic carbon, nitrogen, and sulfur cycling in anoxic environments clustered together in a low-oxygen subnetwork that correlated positively with nitrification N₂O yields and N₂O production from denitrification. Close coupling between N₂O producers and consumers in the anoxic basin is indicated by strong correlations between the low-oxygen subnetwork, PICRUSt2-predicted nitrous oxide reductase (nosZ) gene abundances, and N₂O undersaturation. This study implicates keystone taxa affiliated with common ODZ groups as a potential control on water column N₂O cycling and provides a theoretical basis for further investigations into marine microbial interaction networks.

Metatranscriptomes reveal the diverse responses of Thaumarchaeota ecotypes to environmental variations in the northern slope of the South China Sea

Thaumarchaeota are among the most abundant prokaryotes in the ocean, playing important roles in carbon and nitrogen cycling. Marine Thaumarchaeota ecotypes exhibit depth-related diversification and seasonal changes. However, transcriptomic activities concerning niche partitioning among thaumarchaeal ecotypes remain unclear. Here, we examined the variations in the distribution and transcriptomic activity of marine Thaumarchaeota ecotypes. Three primary ecotypes were identified: a Nitrosopumilus-like clade; a Nitrosopelagicus-like water column A (WCA) clade, thriving in epipelagic water; and a water column B (WCB) clade, dominant in deep water. Depth-related partitioning of the three ecotypes and the seasonal variability of the WCA and WCB ecotypes were observed. Nutrient concentrations, chlorophyll α and salinity were the primary environmental factors. The relative abundance of the WCA ecotype and its transcript abundance of amoA gene were positively correlated with chlorophyll α and salinity, while the WCB ecotype was positively correlated with nitrate and phosphate. Based on high-quality metagenome-assembled genomes, transcriptomic analysis revealed that the three ecotypes exhibited various co-occurring expression patterns of the elemental cycling genes in the nitrogen, carbon, phosphorus, and sulfur cycles. Our results provide transcriptomic evidence of the niche differentiation of marine Thaumarchaeota ecotypes, highlighting the diverse roles of ecotypes and WCA subclades in biogeochemical cycles.

Phylogenetic divergence and adaptation of Nitrososphaeria across lake depths and freshwater ecosystems

Thaumarchaeota (now the class Nitrososphaeria in the phylum Thermoproteota in GTDB taxonomy) are abundant across marine and soil habitats; however, their genomic diversity and evolutionary history in freshwater environments remain elusive. Here, we reconstructed 17 high-quality metagenome-assembled genomes of Nitrososphaeria from a deep lake and two great rivers, and compared all available genomes between freshwater and marine habitats regarding their phylogenetic positions, relative abundance, and genomic content. We found that freshwater Nitrososphaeria were dominated by the family Nitrosopumilaceae and could be grouped into three distinct clades closely related to the genera Nitrosopumilus, Nitrosoarchaeum, and Nitrosotenuis. The Nitrosopumilus-like clade was exclusively from deep lakes, while the Nitrosoarchaeum-like clade was dominated by species from deep lakes and rivers, and the Nitrosotenuis-like clade was mainly from rivers, deep lakes, and estuaries. Interestingly, there was vertical niche separation between two clades in deep lakes, showing that the Nitrosopumilus-like species dominated shallow layers, whereas the relative abundance of the Nitrosoarchaeum-like clade increased toward deep waters. Phylogenetic clustering patterns in the Nitrosopumilaceae supported at least one freshwater-to-marine and two marine-to-freshwater transitions, the former of which refined the potential terrestrial-to-marine evolutionary path as previously proposed. The occurrence of the two marine-to-freshwater transitions were accompanied by horizontal transfer of the genes involved in nutrition regulation, osmoregulation, and cell motility during their colonization to freshwater habitats. Specifically, the Nitrosopumilus-like clade showed losses of genes encoding flagella assembly and ion transport, whereas the Nitrosoarchaeum-like clade had losses of intact genes involved in urea uptake and utilization and gains of genes encoding osmolarity-mediated mechanosensitive channels. Collectively, our results reveal for the first time the high genomic diversity of the class Nitrososphaeria across freshwater ecosystems and provide novel insights into their adaptive mechanisms and evolutionary histories.

Bacterial and archaeal lipids trace chemo(auto)trophy along the redoxcline in Vancouver Island fjords

Marine oxygen minimum zones play a crucial role in the global oceanic carbon, nitrogen, and sulfur cycles as they harbor microbial communities that are adapted to the water column chemistry and redox zonation, and in turn control the water column chemistry and greenhouse gas release. These micro-organisms have metabolisms that rely on terminal electron acceptors other than O₂ and often benefit from syntrophic relationships (metabolic coupling). Here, we study chemo(auto)trophy along the redoxcline in two stratified fjords on Vancouver Island (Canada) using bacterial bacteriohopanepolyols and archaeal ether lipids. We analyze the distribution of these lipid classes in suspended particulate matter (SPM) to trace ammonia oxidation, anaerobic ammonium oxidation (anammox), sulfate reduction/sulfur oxidation, methanogenesis, and methane oxidation, and investigate ecological niches to evaluate potential links between their respective bacterial and archaeal sources. Our results show an unparalleled BHP and ether lipid structural diversity that allows tracing the major redox-driven metabolic processes at the time of sampling: Both fjords are dominated by archaeal ammonia oxidation and anammox; sulfate-reducing bacteria may be present in Deer Bay, but absent from Effingham Inlet; methanogenic Euryarchaeota and archaeal and bacterial methanotrophs are detectable at low abundance. Correlation analysis reveals distinct biomarker clusters that provide constraints on the biogeochemical niches of some orphan BHP and ether lipids such as in situ-produced adenosyl-BHPs or unsaturated archaeols.

Depth-Differentiation and Seasonality of Planktonic Microbial Assemblages in the Monterey Bay Upwelling System

Coastal upwelling regions are hotspots of biological productivity, supporting diverse communities of microbial life and metabolisms. Monterey Bay (MB), a coastal ocean embayment in central California, experiences seasonal upwelling of cold, nutrient-rich waters that sustain episodes of high phytoplankton production in surface waters. While productivity in surface waters is intimately linked to metabolisms of diverse communities of Archaea and Bacteria, a comprehensive understanding of the microbial community in MB is missing thus far, particularly in relation to the distinct hydrographic seasons characteristic of the MB system. Here we present the results of a 2-year microbial time-series survey in MB, investigating community composition and structure across spatiotemporal gradients. In deciphering these patterns, we used unique sequence variants (SVs) of the 16S rRNA gene (V4–V5 region), complemented with metagenomes and metatranscriptomes representing multiple depth profiles. We found clear depth-differentiation and recurring seasonal abundance patterns within planktonic communities, particularly when analyzed at finer taxonomic levels. Compositional changes were more pronounced in the upper 0–40 m of the water column, whereas deeper depths were characterized by temporally stable populations. In accordance with the dynamic nutrient profiles, the system appears to change from a Bacteroidetes- and Rhodobacterales-dominated upwelling period to an oceanic season dominated by oligotrophic groups such as SAR11 and picocyanobacteria. The cascade of environmental changes brought about by upwelling and relaxation events thus impacts microbial community structure in the bay, with important implications for the temporal variability of nutrient and energy fluxes within the MB ecosystem. Our observations emphasize the need for continued monitoring of planktonic microbial communities in order to predict and manage the behavior of this sensitive marine sanctuary ecosystem, over projected intensification of upwelling in the region.

Metagenome-assembled genomes reveal unique metabolic adaptations of a basal marine Thaumarchaeota lineage

Thaumarchaeota constitute an abundant and ubiquitous phylum of Archaea that play critical roles in the global nitrogen and carbon cycles. Most well-characterized members of the phylum are chemolithoautotrophic ammonia-oxidizing archaea (AOA), which comprise up to 5 and 20% of the total single-celled life in soil and marine systems, respectively. Using two high-quality metagenome-assembled genomes (MAGs), here we describe a divergent marine thaumarchaeal clade that is devoid of the ammonia-oxidation machinery and the AOA-specific carbon-fixation pathway. Phylogenomic analyses placed these genomes within the uncultivated and largely understudied marine pSL12-like thaumarchaeal clade. The predominant mode of nutrient acquisition appears to be aerobic heterotrophy, evidenced by the presence of respiratory complexes and various organic carbon degradation pathways. Both genomes encoded several pyrroloquinoline quinone (PQQ)-dependent alcohol dehydrogenases, as well as a form III RuBisCO. Metabolic reconstructions suggest anaplerotic CO₂ assimilation mediated by RuBisCO, which may be linked to the central carbon metabolism. We conclude that these genomes represent a hitherto unrecognized evolutionary link between predominantly anaerobic basal thaumarchaeal lineages and mesophilic marine AOA, with important implications for diversification within the phylum Thaumarchaeota.