Biology subjects

Orellana, L. H.

Publications and source records attributed to Orellana, L. H..

7 recordsLinked to original sources

bioRxiv2026

Metagenomic insights into microbial mediation of Caulerpa prolifera invasion in a coastal lagoon

Opportunistic seaweeds of the genus Caulerpa have benefited from human-driven environmental change to expand within coastal lagoons, frequently displacing native seagrasses. In the Mar Menor lagoon (southeastern Spain), Caulerpa prolifera has progressively expanded since the 1970s, coinciding with the decline of the native seagrass Cymodocea nodosa. Sediments colonized by Ca. prolifera are characterized by elevated sulfide concentrations, which are toxic to seagrasses. Because sulfide is microbially produced, these sediment communities likely shape the competition between Ca. prolifera and Cy. nodosa. However, their metabolic potential and activity remain poorly understood. Here, we examined the taxonomic composition and functional capabilities of sediment microbial communities using 12 paired metagenomes and metatranscriptomes from areas dominated by either Ca. prolifera or Cy. nodosa. Caulerpa-associated sediments displayed a higher potential for organic matter degradation and sulfate reduction. Several metagenome-assembled genomes (MAGs) encoded enzymes putatively involved in the degradation of pectin-like polysaccharides characteristic of the Caulerpa cell wall. Comparison of metagenomic and metatranscriptomic data further revealed that the most abundant MAGs were not necessarily the most transcriptionally active. This finding challenges the common assumption that ecological importance is primarily determined by abundance and highlights the potential contribution of less abundant microorganisms to biogeochemical cycling. Further, 97 of the 100 most highly expressed genes lacked functional annotation. Recombinant production and functional characterization of the protein encoded by the most highly expressed gene in the analyzed sediments revealed that it is an enzyme able to breakdown endogenous bacterial peptidoglycan. Collectively, these results underscore the importance of integrating metagenomics and metatranscriptomics with experimental validation to achieve a more comprehensive understanding of microbial functional capabilities, an integration that is still uncommon in the microbial ecology field.

microbiology↗

bioRxiv2024

Deep long-read metagenomic sequencing reveals niche differentiation in carbon cycling potential between benthic and planktonic microbial populations

Coastal marine sediments function as large-scale natural biocatalytic filters, remineralizing and transforming organic matter. Benthic microbiomes exhibit remarkable temporal stability, contrasting with the dynamic, substrate-driven successions of bacterioplankton. Nonetheless, understanding their role in carbon cycling and interactions between these microbial groups is limited due to the complexity of benthic microbiomes. Here, we used a seasonally resolved, deep short- and long-read metagenomic approach to examine distinctive genomic features of microbiomes recovered from sediment, the overlaying water column, and particle-attached bacteria and archaea in the North Sea. We recovered 115 benthic metagenome-assembled genomes (MAGs) that belonged to Woeseiales, Rhizobiales, Planctomycetia, Gemmatimonadota, and Desulfobacterota species. While Proteobacteria and Actinobacteriota were characteristic phyla of sediments, Acidimicrobiia and Desulfocapsaceae species were shared between sediments and particle-attached fractions of the water column, indicative of significant bentho-pelagic coupling. Predominant members of the family Woeseiaceae carried polysaccharide utilization loci (PULs) predicted to target laminarin, alginate, and -glucan in sediments. In contrast, water column species lacked PULs and encoded a significantly higher fraction of sulfatases and peptidases, indicating a role in the degradation of protein-rich and sulfated organic matter. Our findings disentangle family-level adaptations and niche differentiation between globally significant benthic and water column populations involved in marine organic matter degradation and carbon storage.

microbiology↗

bioRxiv2024

Phosphate starvation stops bacteria digesting algal fucan that sequesters carbon

Algae provide a solar powered pathway to capture and sequester carbon by injecting stable fucan made from carbon dioxide into the ocean 1-4. Stability of the pathway is at odds with the presence of marine bacteria with genes of enzymes that can digest fucan and release the carbon dioxide 5. Biochemical explanations for stable fucan remain hypothetical 6. We assembled a biological carbon cycle model and found phosphate limitation enhanced fucan synthesis by algae, stopped digestion by bacteria and thereby stabilized the fucan carbon sequestration pathway. Marine microalgae Glossomastix sp. PLY432 increased synthesis of fucan, a part of its extracellular matrix, under nutrient-growth limiting conditions. Rate and extent of fucan digestion by a marine, isolated bacterium of the Akkermansiaceae family decreased with decreasing phosphate concentration. Phosphate starvation restricted bacterial growth rate, biomass yield and in turn increased the amount of stable fucan. Phosphate is universally required for growth but rare relative to glycan carbon in photosynthesis-derived ecosystems. The fact that phosphate is required for replication, transcription and translation explains why bacteria can digest gigatons of laminarin with a few enzymes, but not fucan during nutrient limited algal blooms. We conclude phosphate starvation constrains the ability of bacteria to digest fucan, which evolves to maintain stability around algal cells and consequentially also to keep carbon dioxide in the ocean.

microbiology↗

bioRxiv2021

Metagenome-based comparisons of decay rates and host-specificity of fecal microbial communities for improved microbial source tracking

Fecal material in the environment is a primary source of pathogens that cause waterborne diseases and affect over a billion people worldwide. Microbial source tracking (MST) assays based on single genes (e.g., 16S rRNA) do not always provide the resolution needed to attribute fecal contamination sources. In this work, we used dialysis bag mesocosms simulating a freshwater habitat that were spiked separately with cow, pig, or human feces to monitor the decay of host-specific fecal signals over time with metagenomics, traditional qPCR, and culture-based methods. Sequencing of the host fecal communities used as inocula recovered 79 non-redundant metagenome-assembled genomes (MAGs) whose abundance patterns showed that the majority of the fecal community signal was not detectable in the mesocosm metagenomes after four days. Several MAGs showed high host specificity, and thus are promising candidates for biomarkers for their respective host type. Traditional qPCR methods varied in their correlation with MAG decay kinetics. Notably, the human-specific Bacteroides assay, HF183/BFDRev, consistently under-estimated fecal pollution due to not being present in all hosts and/or primer mismatches. This work provides new insights on the persistence and decay kinetics of host-specific gut microbes in the environment and identifies several MAGs as putative biomarkers for improved MST. SYNOPSISWe track cow, pig, and human fecal pollution in lake water over time with metagenomics and benchmark these novel protocols against standard culture-based and qPCR tests for water quality monitoring.

microbiology↗

bioRxiv2020

Metagenomic characterization of soil microbial communities in the Luquillo experimental forest (Puerto Rico) and implications for nitrogen cycling

The phylogenetic and functional diversity of microbial communities in tropical rainforests, and how these differ from temperate communities remain poorly described but are directly related to the increased fluxes of greenhouse gases such as nitrous oxide (N2O) from the tropics. Towards closing these knowledge gaps, we analyzed replicated shotgun metagenomes representing distinct life zones from four locations in the Luquillo Experimental Forest (LEF), Puerto Rico. These soils had a distinct microbial community composition and lower species diversity when compared to temperate grasslands or agricultural soils. Unlike temperate soils, LEF soils showed little stratification with depth in the first 0-30cm, with ~45% of community composition differences explained solely by location. The relative abundances and nucleotide sequences of N2O reductases (nosZ) were highly similar between tropical forest and temperate soils. However, respiratory NO reductase (norB) was 2-fold more abundant in the tropical soils, which might be relatable to their greater N2O emissions. Nitrogen fixation (nifH) also showed higher relative abundance in rainforest compared to temperate soils (20% vs. 0.1-0.3% of bacterial genomes in each soil type harbored the gene, respectively). Collectively, these results advance our understanding of spatial diversity and metabolic repertoire of tropical rainforest soil communities, and should facilitate future ecological modeling efforts. ImportanceTropical rainforests are the largest terrestrial sinks of atmospheric CO2 and the largest natural source of N2O emissions, two critical greenhouse gases for the climate. The microbial communities of rainforest soils that directly or indirectly, through affecting plant growth, contribute to these fluxes remain poorly described by cultured-independent methods. To close this knowledge gap, the present study applied shotgun metagenomics to samples selected from 3 distinct life zones within the Puerto Rico rainforest. The results advance our understanding of microbial community diversity in rainforest soils and should facilitate future studies of natural or manipulated perturbations of these critical ecosystems.

microbiology↗

bioRxiv2019

Metagenomic characterization of creek sediment microbial communities from a major agricultural region in Salinas, California

Little is known about the public health risks associated with natural creek sediments that are affected by runoff and fecal pollution from agricultural and livestock practices. For instance, the persistence of foodborne pathogens originating from agricultural activities such as Shiga Toxin-producing E. coli (STEC) in such sediments remains poorly quantified. Towards closing these knowledge gaps, the water-sediment interface of two creeks in the Salinas River Valley was sampled over a nine-month period using metagenomics and traditional culture-based tests for STEC. Our results revealed that these sediment communities are extremely diverse and comparable to the functional and taxonomic diversity observed in soils. With our sequencing effort (~4 Gbp per library), we were unable to detect any pathogenic Escherichia coli in the metagenomes of 11 samples that had tested positive using culture-based methods, apparently due to relatively low pathogen abundance. Further, no significant differences were detected in the abundance of human- or cow-specific gut microbiome sequences compared to upstream, more pristine (control) sites, indicating natural dilution of anthropogenic inputs. Notably, a high baseline level of metagenomic reads encoding antibiotic resistance genes (ARGs) was found in all samples and was significantly higher compared to ARG reads in metagenomes from other environments, suggesting that these communities may be natural reservoirs of ARGs. Overall, our metagenomic results revealed that creek sediments are not a major sink for anthropogenic runoff and the public health risk associated with these sediment microbial communities may be low.\n\nIMPORTANCECurrent agricultural and livestock practices contribute to fecal contamination in the environment and the spread of food and water-borne disease and antibiotic resistance genes (ARGs). Traditionally, the level of pollution and risk to public health is assessed by culture-based tests for the intestinal bacterium, E. coli. However, the accuracy of these traditional methods (e.g., low quantification, and false positive signal when PCR-based) and their suitability for sediments remains unclear. We collected sediments for a time series metagenomics study from one of the most highly productive agricultural regions in the U.S. in order to assess how agricultural runoff affects the native microbial communities and if the presence of STEC in sediment samples can be detected directly by sequencing. Our study provided important information on the potential for using metagenomics as a tool for assessment of public health risk in natural environments.

microbiology↗

bioRxiv2018

Comparing DNA, RNA and protein levels for measuring microbial activity in nitrogen-amended soils

Multi-omic techniques can offer a comprehensive overview of microbial communities at the gene, transcript and protein levels. However, to what extent these levels reflect in situ process rates is less clear, especially in highly complex habitats such as soils. Here we performed microcosm incubations using soil from a site with a history of agricultural management. Microcosms, amended with isotopically labelled ammonium and urea to simulate a fertilization event, showed nitrification (up to 4.1 {+/-} 0.87 {micro}g N-NO3- g-1 dry soil d-1) and accumulation of N2O after 192 hours of incubation. Nitrification activity (NH4+[->]NH2OH[->]NO2-[->]NO3-) was accompanied by a 6-fold increase in relative expression of the 16S rRNA gene (RNA/DNA) between 10 and 192 hours of incubation for ammonia-oxidizing bacteria (AOB) Nitrosomonas and Nitrosospira. In contrast, ammonia-oxidizing archaea (AOA) and complete ammonia oxidizer (comammox) nitrifiers showed stable gene expression during incubations but were generally more abundant (DNA level) than their Betaproteobacteria AOB counterparts. A strong relationship between nitrification activity and (mostly) betaproteobacterial ammonia monooxygenase (amoA; NH4+[->]NH2OH) and nitrite oxidoreductase (nxrA; NO2-[->]NO3-) transcript abundances revealed that mRNA levels quantitatively reflected measured activity and were generally more sensitive than the DNA level in the microcosm incubations. Although peptides related to housekeeping proteins from nitrite-oxidizing microorganisms were detected, their abundance was not significantly correlated with activity, revealing that meta-proteomics provided only a qualitative assessment of activity. Altogether, these findings underscore the strengths and limitations of multi-omic approaches for assessing complex microbial communities and provide the molecular means to assess nitrification processes in soils.\n\nIMPORTANCEEven though the use of omic approaches has expanded our knowledge of the diversity of microbial communities in natural and engineered systems, it is less clear how well the use of whole community DNA-, RNA- or protein-based approaches reflect microbial activities. To this end, we directly compared the different levels of molecular information (i.e., DNA, RNA or proteins) in order to assess which level best correlated with isotope-based measurements of nitrification activity in agricultural soils after fertilization. This work reveals the strengths as well as the associated limitations of metagenomic, metatranscriptomic, and metaproteomic approaches in serving as reliable proxies for examining microbial activities in highly diverse environments like soils.

microbiology↗