Biology subjects

Baltar, F.

Publications and source records attributed to Baltar, F..

8 recordsLinked to original sources

bioRxiv2024

Illuminating microbial phosphorus cycling in deep-sea cold seep sediments using protein language models

Phosphorus is essential for life and critically influences marine productivity. Despite geochemical evidence of active phosphorus cycling in deep-sea cold seep ecosystems, the microbial processes involved remain poorly understood. Traditional sequence-based searches often fail to detect proteins with remote homology. To address this, we developed a protein language model (PLM) named LucaPCycle that integrates sequence and structural information. This PLM-based approach identified 4,606 new phosphorus-cycling protein families based on the non-redundant gene and genome catalogs from global cold seeps, substantially enhancing our understanding of their diversity, ecology, and function. Among previously unannotated sequences, we discovered three novel alkaline phosphatase families (ALP1, ALP2 and ALP3) that feature unique domain organizations and preserved enzymatic capabilities. These results highlight previously overlooked ecological importance of phosphorus cycling within cold seeps, corroborated by data from porewater geochemistry, metatranscriptomics, and metabolomics. We identified a previously unrecognized diversity of archaea contributing to organic phosphorus mineralization and inorganic phosphorus solubilization through various mechanisms. This includes ecologically significant groups such as Asgardarchaeota, anaerobic methanotrophic archaea (ANME), and Thermoproteota. Additionally, viruses can enhance their hosts (e.g., ANME) phosphorus utilization through the PhoR-PhoB regulatory system and PhnCDE transporter, indirectly influencing methane dynamics. Overall, our PLM-based functional predictions are capable of accessing previously hidden sequence spaces for microbial phosphorus cycling, and can be applied to other various ecosystems.

microbiology↗

bioRxiv2022

Salp blooms increase carbon export 5-fold in the Southern Ocean

The Southern Ocean (SO) contributes substantially to the global biological carbon pump (BCP). Salps in the SO, in particular Salpa thompsoni, are keystone grazers that produce large, fast-sinking fecal pellets with high export potential. In a first study of this kind, we conducted Lagrangian experiments to quantify the salp bloom impacts on export pathways by contrasting locations differing in salp bloom presence/absence. We show that blooms increased particle export by ~5-fold, and exported up to 46% of net primary production out of the euphotic zone. BCP efficiency increased from 5% in non-salp areas to up to 28% in salp areas, which is among the highest recorded in the global ocean. Using SO salp abundances from KRILLBASE, we estimate they can consume ~ 13% of regional production, mediating 13-40% of the SO BCP. Consideration in models forecasting the SO BCP is recommended considering long-term increases in SO salp abundances.

ecology↗

bioRxiv2022

Molecular hydrogen is an overlooked energy source for marine bacteria

Molecular hydrogen (H2) and carbon monoxide (CO) are supersaturated in seawater relative to the atmosphere and hence are readily accessible energy sources for marine microbial communities. Yet while marine CO oxidation is well-described, it is unknown whether seawater communities consume H2. Here we integrated genome-resolved metagenomics, biogeochemistry, thermodynamic modelling, and culture-based analysis to profile H2 and CO oxidation by marine bacteria. Based on analysis of 14 surface water samples, collected from three locations spanning tropical to subantarctic fronts, three uptake hydrogenase classes are prevalent in seawater and encoded by major marine families such as Rhodobacteraceae, Flavobacteriaceae, and Sphingomonadaceae. However, they are less abundant and widespread than carbon monoxide dehydrogenases. Consistently, microbial communities in surface waters slowly consumed H2 and rapidly consumed CO at environmentally relevant concentrations, with H2 oxidation most active in subantarctic waters. The cell-specific power from these processes exceed bacterial maintenance requirements and, for H2, can likely sustain growth of bacteria with low energy requirements. Concordantly, we show that the polar ultramicrobacterium Sphingopyxis alaskensis grows mixotrophically on H2 by expressing a group 2a [NiFe]-hydrogenase, providing the first demonstration of atmospheric H2 oxidation by a marine bacterium. Based on TARA Oceans metagenomes, genes for trace gas oxidation are globally distributed and are fourfold more abundant in deep compared to surface waters, highlighting that trace gases are important energy sources especially in energy-limited waters. Altogether, these findings show H2 is a significant energy source for marine communities and suggest that trace gases influence the ecology and biogeochemistry of oceans globally.

microbiology↗

bioRxiv2021

Microbial rhodopsins are increasingly favored over chlorophyll in High Nutrient Low Chlorophyll waters

Microbial rhodopsins are simple light-harvesting complexes that, unlike chlorophyll photosystems, have no iron requirements for their synthesis and phototrophic functions. Here we report the first environmental concentrations of rhodopsin along the Subtropical Frontal Zone off New Zealand, where Subtropical waters encounter the iron-limited Subantarctic High Nutrient Low Chlorophyll (HNLC) region. Rhodopsin concentrations were highest in HNLC waters where chlorophyll-a concentrations were lowest. Furthermore, while the ratio of rhodopsin to chlorophyll-a photosystems was on average 20 along the transect, this ratio increased to over 60 in HNLC waters. We further show that microbial rhodopsins are abundant in both picoplankton (0.2-3m) and in the larger (>3m) size fractions of the microbial community containing eukaryotic plankton and/or particle-attached prokaryotes. These findings suggest that rhodopsin phototrophy could be critical for microbial plankton to adapt to resource-limiting environments where photosynthesis and possibly cellular respiration are impaired. Originality-Significance statementHigh Nutrient Low Chlorophyll (HNLC) regimes cover approximately 30% of the global ocean surface and play a crucial role in the Earths carbon cycle. Here we show that microbial rhodopsins are particularly abundant in a HNLC region of the Subantarctic ocean, where chlorophyll abundance is relatively low and photosynthesis and respiration might be impaired due to iron limitation. These data suggest that rhodopsin phototrophy can contribute significantly to the energy budgets of HNLC regions, capturing meaningful amounts of light that cannot be channeled through photosynthesis.

ecology↗

bioRxiv2020

Predation impacts late but not early community assembly in model marine biofilms.

Bottom-up selection plays an important role in microbial community assembly but is unable to account for all observed variance. Other processes like top-down selection (e.g. predation) may be partially responsible for the unexplained variance. However, top-down processes often remain unexplored, especially in interaction with bottom-up selective pressures. We utilised an in situ marine biofilm model system to test the effects of bottom-up (i.e. substrate properties) and top-down (i.e. predator exclusion via 100 {micro}m mesh) selective pressures on community assembly over time (56 days). Community compositions were monitored using 16S and 18S rRNA amplicon sequencing. Wooden substrates promoted heterotrophic growth, while the inert substrates (i.e., plastic, glass, tile) lack of degradable material selected for autotrophs. Early wood communities contained 9-50% more mixotrophs and heterotrophs (e.g. Proteobacteria and Euglenozoa) compared to inert substrates. Inert substrates instead showed twice the autotrophic (e.g. Cyanobacteria and Ochrophyta) abundance. Late communities differed mainly due to exclusion status, as large predators preferably pruned heterotrophs. This resulted in the autotrophic domination of native communities, while high heterotrophic abundance characterised exclusive conditions. Top-down control through exclusion increased explainable variance by 18-53%, depending on community age, leading to increased understanding of the underlying ecological framework that guides microbial community assembly.

ecology↗

bioRxiv2019

Metabolic profiling suggests two sources of organic matter shape microbial activity, but not community composition, in New Zealand fjords

Fjords are semi-enclosed marine systems with unique physical conditions that influence microbial communities structure. Pronounced organic matter and physical condition gradients within fjords provide a natural laboratory for the study of changes in microbial phylogeny and metabolic potential in response to environmental conditions (e.g. depth). In the open ocean new production from photosynthesis supplies organic matter to deeper aphotic layers, sustaining microbial activity. We measured the metabolic diversity and activity of microbial communities in fjords to determine patterns in metabolic potential across and within fjords, and whether these patterns could be explained by community composition modifications. We demonstrated that metabolic potential and activity are shaped by similar parameters as total (prokaryotic and eukaryotic) microbial communities. However, we identified increases in metabolic diversity and potential (but not in community composition) at near bottom (aphotic) sites consistent with the influence of sediments in deeper waters. Thus, while composition and function of the microbial community in the upper water column was likely shaped by marine snow and sinking POM generated by new production, deeper sites were strongly influenced by sediment resuspension of benthic organic matter generated from this or other sources (terrestrial, chemoautotrophic, microbial carbon loop), uncoupling the community composition and function dynamics.

ecology↗

bioRxiv2019

Depth and location influence prokaryotic and eukaryotic microbial community structure in New Zealand fjords

Systems with strong horizontal and vertical gradients, such as fjords, are useful models for studying environmental forcing. Here we examine microbial (prokaryotic and eukaryotic) community changes associated with the surface low salinity layer (LSL) and underlying seawater in multiple fjords in Fiordland National Park (New Zealand). High rainfall (1200-8000 mm annually) and linked runoff from native forested catchments results in surface LSLs with high tannin concentrations within each fjord. These gradients are expected to drive changes in microbial communities. We used amplicon sequencing (16S and 18S) to assess the impact of these gradients on microbial communities and identified depth linked changes in diversity and community structure. With increasing depth we observed significant increases in Proteobacteria (15%) and SAR (37%), decreases in Opisthokonta (35%), and transiently increased Bacteroidetes (3% increase from 0 to 40 m, decreasing by 8% at 200 m). Community structure differences were observed along a transect from inner to outer regions, specifically 25% mean relative abundance decreases in Opisthokonta and Bacteroidetes, and increases in SAR (25%) and Proteobacteria (>5%) at the surface, indicating changes based on distance from the ocean. This provides the first in-depth view into the ecological drivers of microbial communities within New Zealand fjords.

ecology↗

bioRxiv2017

Are oceanic fronts ecotones? Seasonal changes along the Subtropical Front show fronts as bacterioplankton transition zones but not diversity hotspots

Ecotones are regarded as diversity hotspots in terrestrial systems, but it is unknown if this \"ecotone effect\" occurs in the marine environment. Oceanic fronts are widespread mesoscale features, present in the boundary between different water masses, and are arguably the best potential examples of ecotones in the ocean. Here we performed the first seasonal study along an oceanic front, combining 16S rRNA gene sequencing coupled with a high spatial resolution analysis of the physical properties of the water masses. Using the Subtropical Frontal Zone off New Zealand we demonstrate that fronts delimit shifts in bacterioplankton community composition between water masses, but that the strength of this effect is seasonally dependent. While creating a transition zone where physicochemical parameters and bacterioplankton communities get mixed, this ecotone does not result in increased diversity. Thus unlike terrestrial ecotones, oceanic ecotones like fronts are boundaries but not hotspot of bacterioplankton diversity in the ocean.

microbiology↗