No abstract

Glacial retreat is changing biogeochemical cycling in the Arctic, where glacial runoff contributes iron for oceanic shelf primary production. We hypothesize that in Svalbard fjords, microbes catalyze intense iron and sulfur cycling in loworganic-matter sediments. This is because low organic matter limits sulfide generation, allowing iron mobility to the water column instead of precipitation as iron monosulfides. In this study, we tested this with high-depth-resolution 16S rRNA gene libraries in the upper 20 cm at two sites in Van Keulenfjorden, Svalbard. At the site closer to the glaciers, iron-reducing Desulfuromonadales, iron-oxidizing Gallionella and Mariprofundus, and sulfur-oxidizing Thiotrichales and Epsilonproteobacteria were abundant above a 12-cm depth. Below this depth, the relative abundances of sequences for sulfate-reducing Desulfobacteraceae and Desulfobulbaceae increased. At the outer station, the switch from iron-cycling clades to sulfate reducers occurred at shallower depths (ϳ5 cm), corresponding to higher sulfate reduction rates. Relatively labile organic matter (shown by ␦ 13 C and C/N ratios) was more abundant at this outer site, and ordination analysis suggested that this affected microbial community structure in surface sediments. Network analysis revealed more correlations between predicted iron-and sulfur-cycling taxa and with uncultured clades proximal to the glacier. Together, these results suggest that complex microbial communities catalyze redox cycling of iron and sulfur, especially closer to the glacier, where sulfate reduction is limited due to low availability of organic matter. Diminished sulfate reduction in upper sediments enables iron to flux into the overlying water, where it may be transported to the shelf. IMPORTANCE Glacial runoff is a key source of iron for primary production in the Arctic. In the fjords of the Svalbard archipelago, glacial retreat is predicted to stimulate phytoplankton blooms that were previously restricted to outer margins. Decreased sediment delivery and enhanced primary production have been hypothesized to alter sediment biogeochemistry, wherein any free reduced iron that could potentially be delivered to the shelf will instead become buried with sulfide generated through microbial sulfate reduction. We support this hypothesis with sequencing data that showed increases in the relative abundance of sulfate reducing taxa and sulfate reduction rates with increasing distance from the glaciers in Van Keulenfjorden, Svalbard. Community structure was driven by organic geochemistry, suggesting that enhanced input of organic material will stimulate sulfate reduction in interior fjord sediments as glaciers continue to recede.

Acidobacteriota are widespread and often abundant in marine sediments, yet their metabolic and ecological properties are poorly understood. Here, we examined metabolisms and distributions of Acidobacteriota in marine sediments of Svalbard by functional predictions from metagenome-assembled genomes (MAGs), amplicon sequencing of 16S rRNA and dissimilatory sulfite reductase (dsrB) genes and transcripts, and gene expression analyses of tetrathionate-amended microcosms. Acidobacteriota were the second most abundant dsrB-harboring (averaging 13%) phylum after Desulfobacterota in Svalbard sediments, and represented 4% of dsrB transcripts on average. Meta-analysis of dsrAB datasets also showed Acidobacteriota dsrAB sequences are prominent in marine sediments worldwide, averaging 15% of all sequences analysed, and represent most of the previously unclassified dsrAB in marine sediments. We propose two new Acidobacteriota genera, Candidatus Sulfomarinibacter (class Thermoanaerobaculia, “subdivision 23”) and Ca. Polarisedimenticola (“subdivision 22”), with distinct genetic properties that may explain their distributions in biogeochemically distinct sediments. Ca. Sulfomarinibacter encode flexible respiratory routes, with potential for oxygen, nitrous oxide, metal-oxide, tetrathionate, sulfur and sulfite/sulfate respiration, and possibly sulfur disproportionation. Potential nutrients and energy include cellulose, proteins, cyanophycin, hydrogen, and acetate. A Ca. Polarisedimenticola MAG encodes various enzymes to degrade proteins, and to reduce oxygen, nitrate, sulfur/polysulfide and metal-oxides. 16S rRNA gene and transcript profiling of Svalbard sediments showed Ca. Sulfomarinibacter members were relatively abundant and transcriptionally active in sulfidic fjord sediments, while Ca. Polarisedimenticola members were more relatively abundant in metal-rich fjord sediments. Overall, we reveal various physiological features of uncultured marine Acidobacteriota that indicate fundamental roles in seafloor biogeochemical cycling.

Subducting oceanic crusts release fluids rich in biologically relevant compounds into the overriding plate, fueling subsurface chemolithoautotrophic ecosystems. To understand the impact of subsurface geochemistry on microbial communities, we collected fluid and sediments from 14 natural springs across a ~200 km transect across the Costa Rican convergent margin and performed shotgun metagenomics. The resulting 404 metagenome-assembled genomes (MAGs) cluster into geologically distinct regions based on MAG abundance patterns: outer forearc-only (25% of total relative abundance), forearc/arc-only (38% of total relative abundance), and delocalized (37% of total relative abundance) clusters. In the outer forearc, Thermodesulfovibrionia, Candidatus Bipolaricaulia, and Firmicutes have hydrogenotrophic sulfate reduction and Wood-Ljungdahl (WL) carbon fixation pathways. In the forearc/arc, Anaerolineae, Ca. Bipolaricaulia, and Thermodesulfovibrionia have sulfur oxidation, nitrogen cycling, microaerophilic respiration, and WL, while Aquificae have aerobic sulfur oxidation and reverse tricarboxylic acid carbon fixation pathway. Transformation-based canonical correspondence analysis shows that MAG distribution corresponds to concentrations of aluminum, iron, nickel, dissolved inorganic carbon, and phosphate. While delocalized MAGs appear surface-derived, the subsurface chemolithoautotrophic, metabolic, and taxonomic landscape varies by the availability of minerals/metals and volcanically derived inorganic carbon. However, the WL pathway persists across all samples, suggesting that this versatile, energy-efficient carbon fixation pathway helps shape convergent margin subsurface ecosystems.

Environmental fluctuations are recorded in a variety of sedimentary archives of lacustrine depositional systems. Geochemical signals recovered from bottom sediments in closed‐basin lakes are among the most sensitive paleoenvironmental indicators and are commonly used in reconstructing lake evolution. Microbialites (i.e., organosedimentary deposits accreted through microbial trapping and binding of detrital sediment or in situ mineral precipitation on organics [Palaios, 2, 1987, 241]), however, have been largely overlooked as paleoenvironmental repositories. Here, we investigate concentrically laminated mineralized microbialites from Laguna Negra, a high‐altitude (4,100 m above sea level) hypersaline, closed‐basin lake in northwestern Argentina, and explore the potential for recovery of environmental signals from these unique sedimentary archives. Spatial heterogeneity in hydrological regime helps define zones inside Laguna Negra, each with their own morphologically distinct microbialite type. Most notably, platey microbialites (in Zone 3A) are precipitated by evaporative concentration processes, while discoidal oncolites (in Zone 3C) are interpreted result from fluid mixing and biologically mediated nucleation. This spatial heterogeneity is reflected in petrographically distinct carbonate fabrics: micritic, botryoidal, and isopachous. Fabric type is interpreted to reflect a combination of physical and biological influences during mineralization, and paired C‐isotope measurement of carbonate and organic matter supports ecological differences as a dominant control on C‐isotopic evolution between zones. Laminae of Laguna Negra microbialites preserve a range of δ13Ccarb from +5.75‰ to +18.25‰ and δ18Ocarb from −2.04‰ to +9.28‰. Temporal trends of lower carbon and oxygen isotopic compositions suggest that the influence of CO2 degassing associated with evaporation has decreased over time. Combined, these results indicate that microbialite archives can provide data that aid in interpretation of both lake paleohydrology and paleoenvironmental change.

Two common quantification methods for subseafloor microorganisms are catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) and quantitative PCR (qPCR). Using these methods, we quantified Bacteria and Archaea in Baltic Sea basin sediments (IODP Exp. 347) down to 90 mbsf, testing the following hypotheses in an interlaboratory comparison: (1) proteinase K permeabilization of archaeal cell walls increases CARD-FISH accuracy and (2) qPCR varies by more than an order of magnitude between laboratories using similar protocols. CARD-FISH counts did not differ between permeabilization treatments, demonstrating that proteinase K did not increase accuracy of CARD-FISH counts. However, 91% of these counts were below the quantification limit of 1.3 × 107 cells cm-3. For qPCR, data varied between laboratories, but were largely within the same order of magnitude if the same primers were used, with 88% of samples being above the quantification limit. Copy number values were elevated by preparing a sediment slurry before DNA extraction: 3.88 × 106-2.34 × 109 16S rRNA gene copies cm-3 vs. 1.39 × 107-1.87 × 109 total cells cm-3. By qPCR, Bacteria were more abundant than Archaea, although they usually were within the same order of magnitude. Overall, qPCR is more sensitive than CARD-FISH, but both require optimization to consistently achieve both precision and accuracy.

Motivation Metal binding proteins have a central role in maintaining life processes. Nearly one-third of known protein structures contain metal ions that are used for a variety of needs, such as catalysis, DNA/RNA binding, protein structure stability, etc. Identifying metal binding proteins is thus crucial for understanding the mechanisms of cellular activity. However, experimental annotation of protein metal binding potential is severely lacking, while computational techniques are often imprecise and of limited applicability. Results We developed a novel machine learning-based method, mebipred, for identifying metal binding proteins from sequence-derived features. This method is over 80% accurate in recognizing proteins that bind metal ion-containing ligands; the specific identity of eleven ubiquitously-present metal ions can also be annotated. mebipred is reference-free, i.e. no sequence alignments are involved, and is thus faster than alignment-based methods; it also more accurate than other sequence-based prediction methods. Additionally, mebipred can identify protein metal binding capabilities from short sequence stretches, e.g. translated sequencing reads, and, thus, may be useful for the annotation of metal requirements of metagenomic samples. We performed an analysis of available microbiome data and found that ocean, hot spring sediments, and soil microbiomes use a more diverse set of metals than human host-related ones. For human microbiomes, physiological conditions explain the observed metal preferences. Similarly, subtle changes in ocean sample ion concentration affect the abundance of relevant metal binding proteins. These results highlight mebipred’s utility in analysing microbiome metal requirements. Availability mebipred is available as a web server at services.bromberglab.org/mebipred and as a standalone package at https://pypi.org/project/mymetal/. Supplementary information Supplementary data are available from Bioinformatics online repository. Additional data is available from http://dx.doi.org/10.5281/zenodo.5722730 and http://dx.doi.org/10.5281/zenodo.6332940.

Large and growing data resources on the spatial and temporal diversity and distribution of the more than 400 carbon-bearing mineral species reveal patterns of mineral evolution and ecology. Recent advances in analytical and visualization techniques leverage these data and are propelling mineralogy from a largely descriptive field into one of prediction within complex, integrated, multidimensional systems. These discoveries include: (1) systematic changes in the character of carbon minerals and their networks of coexisting species through deep time; (2) improved statistical predictions of the number and types of carbon minerals that occur on Earth but are yet to be discovered and described; and (3) a range of proposed and ongoing studies related to the quantification of network structures and trends, relation of mineral "natural kinds" to their genetic environments, prediction of the location of mineral species across the globe, examination of the tectonic drivers of mineralization through deep time, quantification of preservational and sampling bias in the mineralogical record, and characterization of feedback relationships between minerals and geochemical environments with microbial populations. These aspects of Earth's carbon mineralogy underscore the complex coevolution of the geosphere and biosphere and highlight the possibility for scientific discovery in Earth and planetary systems.