Biology subjects

Morales, S. E.

Publications and source records attributed to Morales, S. E..

16 recordsLinked to original sources

bioRxiv2023

Differences in density: taxonomic but not functional diversity in seaweed microbiomes affected by an earthquake

Host-associated microbial communities can make important contributions to host health, and are shaped by a range of different factors ranging from host condition, environmental conditions, and other microbes. Disentangling the roles of these factors can be particularly difficult as many variables are correlated. Here, we leveraged earthquake-induced changes in host density to identify the influence of host density on microbiome composition. A large (7.8 magnitude) earthquake in New Zealand in 2016 led to widespread coastal uplift of up to ~6m, sufficient to locally extirpate some intertidal kelp populations. These uplifted populations are slowly recovering, but intertidal kelps remain at much lower densities than at nearby, less uplifted sites. By comparing the microbiome of the low and high density sites using 16S amplicon sequencing, we observed that low density populations had higher beta-diversity than high density populations with regards to taxonomic variability, while no beta-diversity differences were observed between functional categories. Using phylogenetic and taxonomic turnover approaches, we determined that dispersal limitation shapes low density populations to a greater extent, while homogeneous selection shapes high density populations to a greater extent. Our findings shed light on microbiome assembly processes, particularly highlighting that large-scale disturbances that affect host density can dramatically influence microbiome structure.

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

High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems

CRISPR-Cas are adaptive immune systems that protect their hosts against viruses and other parasitic mobile genetic elements. Consequently, selection from viruses and other genetic parasites is often assumed to drive the acquisition and maintenance of these immune systems in nature, but this remains untested. Here, we analyse the abundance of CRISPR arrays in natural environments using metagenomic datasets from 332 terrestrial, aquatic and host-associated ecosystems. For each metagenome we quantified viral abundance and levels of viral community diversity to test whether these variables can explain variation in CRISPR-Cas abundance across ecosystems. We find a strong positive correlation between CRISPR-Cas abundance and viral abundance. In addition, when controlling for differences in viral abundance, we found that the CRISPR-Cas systems are more abundant when viral diversity is low. We also found differences in relative CRISPR-Cas abundance among environments, with environmental classification explaining [~]24% of variation in CRISPR-Cas abundance. However, the correlations with viral abundance and diversity are broadly consistent across diverse natural environments. These results indicate that viral abundance and diversity are major ecological factors that drive the selection and maintenance of CRISPR-Cas in microbial ecosystems. Significance statementNumerous studies demonstrate that CRISPR-Cas immune systems can provide defence against bacteriophage and archaeal viruses, yet little is known about the ecological conditions where CRISPR-Cas immunity is favoured. Moreover, our knowledge is largely confined to laboratory studies and it is unknown if viruses are a key selective driver of CRISPR-Cas in nature. Using metagenomic data from diverse environments we find that both viral abundance and the abundance of CRISPR-Cas immune systems correlate positively across most environments. Furthermore, CRISPR-Cas systems are more prevalent when viral diversity is low. These results extend previous theoretical work by demonstrating that viruses are a key driver of selection of CRISPR-Cas immune systems across many natural ecosystems.

microbiology↗

bioRxiv2020

Soil Chemistry and Microbiome Determine N2O Emission Potential in Soils

Microbial nitrogen (N) transformations in soil, notably denitrification, result in the production of the potent greenhouse and ozone depleting gas nitrous oxide (N2O). Soil chemistry and microbiome composition impact N2O emission potential but the relative importance of these factors as determinants of N2O emission in denitrifying systems is rarely tested. In addition, previous linkages between microbiome composition and N2O emission potential rarely demonstrate causality. Here, we determined the relative impact of microbiome composition (i.e. soil extracted cells) and chemistry (i.e. water extractable chemicals) on N2O emission potential utilizing an anoxic cell based assay system. Cells and chemistry for assays were sourced from soils with contrasting N2O/N2O+N2 ratios, combined in various combinations and denitrification gas production was measured in response to nitrate addition. Average directionless effects of cell and chemical extract on N2O/N2O+N2 (Cell: {Delta}0.16, Chemical extract: {Delta}0.22) and total N2O hypothetically emitted (Cell: {Delta}2.62 mol-N, Chemical extract: {Delta}4.14 mol-N) indicated chemistry is the most important determinant of N2O emissions. Independent pH differences of just 0.6 points impacted N2O/N2O+N2 on par with independent chemical extract differences, supporting the dominance of this variable in previous studies. However, impacts on overall N2O hypothetically emitted were smaller suggesting that soil pH manipulation may not necessarily be a successful approach to mitigate emissions over a fixed time period. In addition, we observed increased N2O accumulation and emission potential at the end of incubations concomitant with predicted decreases in carbon availability suggesting that carbon limitation increases N2O emission transiently with the magnitude of emission dependent on the both chemical and microbiome controls.

microbiology↗

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↗

bioRxiv2020

Soil N2O emission potential falls along a denitrification phenotype gradient linked to differences in microbiome, rainfall and carbon availability

Soil denitrification produces the potent greenhouse gas nitrous oxide (N2O) and by further reduction of N2O, the harmless inert gas N2. N2O emission is determined by rate and timing of the N2O producing and reducing steps which are sensitive to a series of proximal and distal regulators such as pH and microbial community composition. Microbial community associations to N2O emission potential (N2O/(N2O+N2)) are commonly entangled with pH leaving the true role of community composition unclear. Here, we leverage a set of soil microbiomes strongly linked to rainfall above pH to test the hypothesis that microbiome vs. N2O emission potential (N2O/(N2O+N2)) correlations will be maintained across alternative distal drivers. N2O emission potential (N2O/(N2O+N2)) and denitrification gas (NO, N2O, N2) kinetics were assessed by automated gas chromatography while community composition was assessed by 16S rRNA gene sequencing and qPCR of nosZI and II genes. Analyses revealed a sustained correlation between microbiome and N2O emission potential (N2O/(N2O+N2)) in the absence of a pH effect. Further, a continuum of gas accumulation phenotypes linked to NO accumulation and sensitive to carbon addition are identified. Separate phenotypes carried out N2O production and reduction steps more concurrently or sequentially and thus determined N2O accumulation and emission potential (N2O/(N2O+N2)). Concurrent N2O producing/reducing soils typically contained NO accumulation to a low steady state, while carbon addition manipulations which increased NO accumulation also increased sequentiality of N2O production/reduction and thus emission potential (N2O/(N2O+N2)). These features may indicate a conserved NO inhibitory mechanism across multiple effectors (rainfall, community composition, carbon availability). HighlightsO_LIN2O emission potential is linked to microbiome changes associated with rainfall, but not to pH. C_LIO_LISequential vs. concurrent denitrification phenotypes differing in NO and N2O accumulation are identified. C_LIO_LIHigh N2O accumulation is associated with increased NO accumulation. C_LIO_LISequentiality of N2O production/reduction determines soil N2O emission potential. C_LIO_LISequentiality of N2O reduction was susceptible to manipulation via carbon addition. C_LI

microbiology↗

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↗

bioRxiv2018

Alternative hydrogen uptake pathways suppress methane production in ruminants

Farmed ruminants are the largest source of anthropogenic methane emissions globally. The methanogenic archaea responsible for these emissions use molecular hydrogen (H2), produced during bacterial and eukaryotic carbohydrate fermentation, as their primary energy source. In this work, we used comparative genomic, metatranscriptomic, and co-culture-based approaches to gain a system-wide understanding of the organisms and pathways responsible for ruminal H2 metabolism. Two thirds of sequenced rumen bacterial and archaeal genomes encode enzymes that catalyze H2 production or consumption, including 26 distinct hydrogenase subgroups. Metatranscriptomic analysis confirmed that these hydrogenases are differentially expressed in sheep rumen. Electron-bifurcating [FeFe]-hydrogenases from carbohydrate-fermenting Clostridia (e.g. Ruminococcus) accounted for half of all hydrogenase transcripts. Various H2 uptake pathways were also expressed, including methanogenesis (Methanobrevibacter), fumarate reduction and nitrate ammonification (Selenomonas), and acetogenesis (Blautia). Whereas methanogenesis predominated in high methane yield sheep, alternative uptake pathways were significantly upregulated in low methane yield sheep. Complementing these findings, we observed significant differential expression and activity of the hydrogenases of the hydrogenogenic cellulose fermenter Ruminococcus albus and the hydrogenotrophic fumarate reducer Wolinella succinogenes in co-culture compared to pure culture. We conclude that H2 metabolism is a more complex and widespread trait among rumen microorganisms than previously recognized. There is evidence that alternative hydrogenotrophs, including acetogens and selenomonads, can prosper in the rumen and effectively compete with methanogens for H2 in low methane yield ruminants. Strategies to increase flux through alternative H2 uptake pathways, including animal selection, dietary supplementation, and methanogenesis inhibitors, may lead to sustained methane mitigation.

microbiology↗

bioRxiv2018

Novel autotrophic organisms contribute significantly to the internal carbon cycling potential of a boreal lake

The authors declare no conflict of interest\n\nFunding sources: the Academy of Finland, Science for Life Laboratories, Tryggers Foundation, the Swedish Research Council VR and the Swedish Foundation for strategic research\n\nAbstractOxygen stratified lakes are typical for the boreal zone, and also a major source of greenhouse gas emissions in the region. Due to shallow light penetration, restricting the growth of phototrophic organisms, and large allochthonous organic carbon inputs from the catchment area, the lake metabolism is expected to be dominated by heterotrophic organisms. In this study we test this assumption and show that the potential for autotrophic carbon fixation and internal carbon cycling is high throughout the water column. Further, we show that during the summer stratification carbon fixation can exceed respiration in a boreal lake even below the euphotic zone. Metagenome assembled genomes and 16S profiling of a vertical transect of the lake revealed multiple organisms in oxygen depleted compartment belonging to novel or poorly characterized phyla. Many of these organisms were chemolithotrophic, deriving their energy from reactions related to sulfur, iron and nitrogen transformations. The community as well as the functions were stratified following the redox potentials. The autotrophic potential in the lake metagenome below the oxygenic zone was high, pointing towards a need for revising our concepts of internal carbon cycling in boreal lakes. Further, the importance of chemolithoautotrophy for the internal carbon cycling suggests that many predicted climate change associated changes in the physical properties of the lake, such as altered mixing patterns, likely have consequences for the whole lake metabolism even beyond the impact to the phototrophic community.\n\nImportanceAutotrophic organisms at the base of the food web are the only life form capable of turning inorganic carbon into organic form, facilitating the survival of all other organisms. In certain environments the autotrophic production is limited by environmental conditions and the food web is supported by carbon coming from outside the ecosystem. One such environment is stratified boreal lakes, which are one of the biggest sources of greenhouse gas emissions in the boreal region. Thus, carbon cycling in these habitats is of outmost importance for the future climate. Here we demonstrate a high potential for internal carbon cycling via phototrophic and novel chemolithotrophic organisms in the dark and anoxic layers of a boreal lake. Our results significantly increase our knowledge on the microbial communities and their metabolic potential in oxygen depleted freshwaters and help to understand and predict how climate change induced alterations could impact the lake carbon dynamics.

ecology↗

bioRxiv2017

Identifying accurate metagenome and amplicon software via a meta-analysis of benchmarking studies

Environmental DNA sequencing has rapidly become a widely-used technique for investigating a range of questions, particularly related to health and environmental monitoring. There has also been a proliferation of bioinformatic tools for analysing metagenomic and amplicon datasets, which makes selecting adequate tools a significant challenge. A number of benchmark studies have been undertaken; however, these can present conflicting results. We have applied a robust Z-score ranking procedure and a network meta-analysis method to identify software tools that are generally accurate for mapping DNA sequences to taxonomic hierarchies. Based upon these results we have identified some tools and computational strategies that produce robust predictions.

bioinformatics↗

bioRxiv2017

Conditionally rare taxa contribute but do not account for prokaryotic community changes in soils

Conditionally rare taxa (CRT) are thought to greatly impact microbial community turnover across many environments, but little is known about their role in soils. Here, we investigate the contribution of CRT to whole community variation over space and time in a series of geographically distinct soils dedicated to three agricultural practices of differing intensities and sampled over a full seasonal cycle. We demonstrate that soil CRT do not account for observed total community changes, but that these rare taxa can be modified by spatiotemporal filters.

microbiology↗

bioRxiv2017

Soil classification predicts differences in prokaryotic communities across a range of geographically distant soils once pH is accounted for

Agricultural land is typically managed based on visible plant life at the expense of the belowground majority. However, microorganisms mediate processes sustaining plant life and the soil environment. To understand the role of microbes we first must understand what controls soil microbial community assembly. We assessed the distribution and composition of prokaryotic communities from soils representing four geographic regions on the South Island of New Zealand. These soils are under three different uses (dairy, sheep and beef, and high country farming) and are representative of major soil classification groups (brown, pallic, gley and recent). We hypothesized that pH would account for major community patterns based on 16S profiles, but that land use and location would be secondary modifiers. Community diversity and structure was linked to pH, coinciding with land use. Soil classification correlated with microbial community structure and evenness, but not richness in high country and sheep and beef communities. The impact of land use and pH remained significant at the regional scale, but soil classification provided support for community variability not explained by either of those factors. These results suggest that several edaphic properties must be examined at multiple spatial scales to robustly examine soil prokaryotic communities.

microbiology↗

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↗

bioRxiv2017

Response to nitrogen addition reveals metabolic and ecological strategies of soil bacteria

The nitrogen (N) cycle represents one of the most well studied systems yet the taxonomic diversity of the organisms that contribute to it is mostly unknown, or linked to poorly characterized microbial groups. While progress has allowed functional groups to be refined, they still rely on a priori knowledge of enzymes involved, and the assumption of functional conservation, with little connection to the role the transformation plays for specific organisms. Here, we use soil microcosms to test the impact of N deposition on prokaryotic communities. By combining chemical, genomic and transcriptomic analysis we are able to identify and link changes in community structure to specific organisms catalyzing given chemical reactions. Urea deposition led to a decrease in prokaryotic richness, and a shift in community composition. This was driven by replacement of stable native populations, which utilize energy from N-linked redox reactions for physiological maintenance, with fast responding populations that use this energy for growth. This model can be used to predict response to N disturbances and allows us to identify putative life strategies of different functional, and taxonomic, groups thus providing insights into how they persist in ecosystems by niche differentiation.

microbiology↗