Biology subjects

Gallego, R.

Publications and source records attributed to Gallego, R..

12 recordsLinked to original sources

bioRxiv2026

Drift-driven microbiome simplification generates reconstructable and ecologically cohesive microbial communities

Engineering simplified microbial communities that retain function and ecological cohesiveness remains a major challenge because the taxa and interactions required for community establishment are rarely known a priori. Here, we experimentally evaluated drift-driven microbiome simplification as an alternative strategy for generating reduced and reconstructable microbial consortia. Using the tomato rhizosphere as a model system, three source microbial communities were subjected to different dilution bottlenecks and serial propagation. Increasing dilution was the main determinant of community composition and simplification, while repeated passage produced additional reductions in ASV richness, phylogenetic diversity, and evenness. Importantly, diversity loss was not accompanied by a uniform deterioration in bacterial colonization or plant performance, indicating that substantial simplification can occur without a parallel collapse in these system-level properties. Candidate Minimal Microbiome prototypes were selected from endpoint communities, reconstructed as synthetic communities, and their ecological cohesiveness was evaluated through invasion experiments. The reconstructed communities strongly restricted the establishment of the original complex microbial fractions, although invasion success depended markedly on invader identity. The drift-derived communities were at least as resistant to invasion as an independently designed bottom-up synthetic community. Together, these results provide experimental support for drift-driven simplification as a strategy to generate reduced microbial communities whose dominant members can be isolated, reconstructed, and experimentally evaluated. By allowing ecological assembly to generate candidate community configurations before cultivation and reconstruction, this approach provides a complementary route to rational bottom-up design and function-directed top-down microbiome engineering.

microbiology↗

bioRxiv2024

Spatial and seasonal biodiversity variation in a large Mediterranean lagoon using environmental DNA metabarcoding through sponge tissue collection

Ecosystem monitoring is a fundamental tool to avert biodiversity loss, gathering valuable information that can be used to develop conservation policies, evaluating management outcomes, and guiding science-based decision-making. The Mar Menor costal lagoon (South-East of Spain) has experienced episodes of eutrophication due to intensive agriculture and other human activities, causing mass mortalities of marine fauna. In this scenario, biodiversity monitoring is crucial to evaluate the status of fauna and flora and take appropriate measures. Here, our main objective was to assess faunal composition and its spatial and temporal structure associated with the pillars used to support the built recreational well-being facilities along the Mar Menor. We capitalised on the many sea sponges that settle on these structures by collecting tissue samples for subsequent extraction of filtered environmental DNA (i.e. natural sampler DNA, nsDNA) in northern and southern areas of the lagoon, both in spring and summer. We metabarcoded all samples at the cytochrome oxidase subunit I gene (COI), and reliably identified 76 taxa belonging to nine different phyla, with annelids, poriferans, molluscs and cnidarians being the richest groups. We detected emblematic species of threatened status, such as pipefishes (genus Syngnathus) and the piddock clam, Pholas dactylus, and others known to become invasive, such as the ascidians Styela canopus and Botrylloides niger, the barnacle Amphibalanus amphitrite, and the polychaetes Branchiomma bairdi and Branchiomma boholense. The use of common and widely distributed sponges as natural eDNA samplers allowed us to characterise both spatial and temporal diversity, further emphasizing the importance of this low-cost approach to monitoring biological communities in shallow coastal ecosystems.

ecology↗

bioRxiv2024

Coupled phylogenetic and functional enrichment in the tomato rhizosphere microbiome

Plant-microbe interactions occur mainly in the rhizosphere, a hot spot of microbial activity and diversity. Given that the outcome of such interactions can significantly impact plant productivity, we require a better understanding of the rhizosphere microbiome if knowledge-based microbiome modification strategies are to be successfully deployed in the future. Here, we aimed to gain a better understanding of the assembly process of the tomato rhizosphere microbiome and its potential composition-function relationships. Among other things, we studied community assembly through the lens of a conceptual framework for the phylogenetically constrained assembly of microbial communities, while assessing community function based on the predicted minimal metagenome of the microbial ecosystem. We observed a systematic enrichment in terms of phylogeny and predicted functional content in the rhizosphere and were able to delimit phylogenetic signal in the ecosystem with 12 functionally coherent phylogenetic groups present in all samples which together accounted for a large fraction of the total community. Our analyses indicated that these groups included a significantly larger content of the ecosystems minimal metagenome than expected by chance. Thus, our study suggests that community assembly followed coupled phylo-functional selection independent of host genetics, and we expect the same phenomenon to occur in other rhizosphere microbiomes. This knowledge provides a thrust in our understanding of how community composition-phylogeny-function relationships drive the assembly process of the rhizosphere microbiome and should help guide the design of synthetic rhizosphere microbiomes for both research and commercial purposes.

microbiology↗

bioRxiv2023

rCRUX: A Rapid and Versatile Tool for Generating Metabarcoding Reference libraries in R

Key to making accurate taxonomic assignments are curated, comprehensive reference barcode databases. However, the generation and curation of such databases has remained challenging given the large and continuously growing volumes of DNA sequence data and novel reference barcode targets. Monitoring and research applications require a greater diversity of specialized gene regions and targeted taxa to meet taxonomic classification goals then are currently curated by professional staff. Thus, there is a growing need for an easy to implement tool that can generate comprehensive metabarcoding reference libraries for any bespoke locus. We address this need by reimagining CRUX from the Anacapa Toolkit and present the rCRUX package in R. The typical workflow involves searching for plausible seed amplicons (get_seeds_local() or get_seeds_remote()) by simulating in silico PCR to acquire seed sequences containing a user-defined primer set. Next these seeds are used to iteratively blast search seed sequences against a local NCBI formatted database using a taxonomic rank based stratified random sampling approach (blast_seeds()) that results in a comprehensive set of sequence matches. This database is dereplicated and cleaned (derep_and_clean_db()) by identifying identical reference sequences and collapsing the taxonomic path to the lowest taxonomic agreement across all matching reads. This results in a curated, comprehensive database of primer specific reference barcode sequences from NCBI. We demonstrate that rCRUX provides more comprehensive reference databases for the MiFish Universal Teleost 12S, Taberlet trnl, and fungal ITS locus than CRABS, METACURATOR, RESCRIPt, and ECOPCR reference databases. We then further demonstrate the utility of rCRUX by generating 16 reference databases for metabarcoding loci that lack dedicated reference database curation efforts. The rCRUX package provides a simple to use tool for the generation of curated, comprehensive reference databases for user-defined loci, facilitating accurate and effective taxonomic classification of metabarcoding and DNA sequence efforts broadly.

bioinformatics↗

bioRxiv2023

Environmental DNA reveals patterns of biological invasion in an inland sea

Non-native species have the potential to cause ecological and economic harm to coastal and estuarine ecosystems. Understanding which habitat types are most vulnerable to biological invasions, where invasions originate, and the vectors by which they arrive can help direct limited resources to prevent or mitigate ecological and socio-economic harm. Information about the occurrence of non-native species can help guide interventions at all stages of invasion, from first introduction, to naturalization and invasion. However, monitoring at relevant scales requires considerable investment of time, resources, and taxonomic expertise. Environmental DNA (eDNA) metabarcoding methods sample coastal ecosystems at broad spatial and temporal scales to augment established monitoring methods. We use COI mtDNA eDNA sampling to survey a diverse assemblage of species across distinct habitats in the Salish Sea in Washington State, USA, and classify each as non-native, native, or indeterminate in origin. The non-native species detected include both well-documented invaders and species not previously reported within the Salish Sea. We find a non-native assemblage dominated by shellfish and algae with native ranges in the temperate western Pacific, and find more-retentive estuarine habitats to be invaded at far higher levels than better-flushed rocky shores. Furthermore, we find an increase in invasion level with higher water temperatures in spring and summer across habitat types. This analysis contributes to a growing understanding of the biotic and abiotic factors that influence invasion level, and underscores the utility of eDNA surveys to monitor biological invasions and to better understand the factors that drive these invasions.

ecology↗

bioRxiv2022

Distinguishing Signal from Noise: Understanding Patterns of Non-Detections to Inform Accurate Quantitative Metabarcoding

Correcting for amplification biases in genetic metabarcoding data can yield quantitative estimates of template DNA concentrations. However, a major source of uncertainty in metabarcoding data is the presence of non-detections, where a technical PCR replicate fails to detect a species observed in other replicates. Such non-detections are an important special case of variability among technical replicates in metabarcoding data, particularly in environmental samples. While many sampling and amplification processes underlie observed variation in metabarcoding data, understanding the causes of non-detections is an important step in distinguishing signal from noise in metabarcoding studies. Here, we use both simulated and empirical data to 1) develop a qualitative understanding of how non-detections arise in metabarcoding data, 2) outline steps to recognize uninformative data in practice, and 3) identify the conditions under which amplicon sequence data can reliably detect underlying biological signals. We show in both simulations and empirical data that, for a given species, the rate of non-detections among technical replicates is a function of both the template DNA concentration and species-specific amplification efficiency. Consequently, we conclude metabarcoding datasets are strongly affected by (1) deterministic amplification biases during PCR and (2) stochastic sampling of amplicons during sequencing -- both of which we can model -- but also by (3) stochastic sampling of rare molecules prior to PCR, which remains a frontier for quantitative metabarcoding. Our results highlight the importance of estimating species-specific amplification efficiencies and critically evaluating patterns of non-detection in metabarcoding datasets to better distinguish environmental signal from the noise inherent in molecular detections of rare targets.

molecular biology↗

bioRxiv2022

Message in a Bottle: Archived DNA Reveals Marine Heatwave-Associated Shifts in Fish Assemblages

Marine heatwaves can drive large-scale shifts in marine ecosystems but studying their impacts on whole species assemblages can be difficult. Here, we leverage the taxonomic breadth and resolution of DNA sequences derived from environmental DNA (eDNA) in the ethanol of a set of 23-year longitudinal ichthyoplankton samples, combining these with microscopy-derived ichthyoplankton identification to yield higher-resolution, species-specific quantitative abundance estimates of fish assemblages in the California Current Large Marine Ecosystem during and after the 2014-16 Pacific marine heatwave. This integrated dataset reveals patterns of tropicalization with increases in southern, mesopelagic species and associated declines in important temperate fisheries targets (e.g., North Pacific Hake (Merluccius productus) and Pacific Sardine (Sardinops sagax)). We observed novel assemblages of southern, mesopelagic fishes and temperate species (e.g., Northern Anchovy, Engraulis mordax) even after the return to average water temperatures. Our innovative preservative derived eDNA metabarcoding and quantitative modeling approaches open the door to reconstructing the historical dynamics of assemblages from modern and archived samples worldwide. SummaryNovel quantitative abundance estimates from archived DNA reveals marine heatwave-associated shifts in fish assemblages.

ecology↗

bioRxiv2022

Toward Quantitative Metabarcoding

Amplicon-sequence data from environmental DNA (eDNA) and microbiome studies provides important information for ecology, conservation, management, and health. At present, amplicon-sequencing studies - known also as metabarcoding studies, in which the primary data consist of targeted, amplified fragments of DNA sequenced from many taxa in a mixture - struggle to link genetic observations to underlying biology in a quantitative way, but many applications require quantitative information about the taxa or systems under scrutiny. As metabarcoding studies proliferate in ecology following decades of microbial and microbiome work using similar techniques, it becomes more important to develop ways ot make them quantitative to ensure that their conclusions are adequately supported. Here we link previously disparate sets of techniques for making such data quantitative, showing that the underlying PCR mechanism explains observed patterns of amplicon data in a general way. By modeling the process through which amplicon-sequence data arises, rather than transforming the data post-hoc, we show how to estimate the starting DNA proportions from a mixture of many taxa. We illustrate how to calibrate the model using mock communities and apply the approach to simulated data and a series of empirical examples. Our approach opens the door to improve the use of metabarcoding data in a wide range of applications in ecology, public health, and related fields.

ecology↗

bioRxiv2020

Environmental DNA Metabarcoding Reveals Winners and Losers of Global Change in Coastal Waters

2Studies of the ecological effects of global change often focus on one or few species at a time. Consequently, we know relatively little about the changes underway at real-world scales of biological communities, which typically have hundreds or thousands of interacting species. Here, we use monthly samples of environmental DNA to survey 222 planktonic taxa along a gradient of temperature, salinity, dissolved oxygen, and carbonate chemistry in nearshore marine habitat. The result is a high-resolution picture of changes in ecological communities using a technique replicable across a wide variety of ecosystems. We estimate community-level differences associated with time, space and environmental variables, and use these results to forecast near-term community changes due to warming and ocean acidification. We find distinct communities in warmer and more acidified conditions, with overall reduced richness in diatom assemblages and increased richness in dinoflagellates. Individual taxa finding greater suitable habitat in near-future waters are more taxonomically varied and include the ubiquitous coccolithophore Emiliania huxleyi and the harmful dinoflagellate Alexandrium sp. These results suggest foundational changes for nearshore food webs under near-future conditions.

ecology↗

bioRxiv2020

Environmental DNA Metabarcoding for Simultaneous Monitoring and Ecological Assessment of Many Harmful Algae

Harmful algae can have profound economic, environmental, and social consequences. As the timing, frequency, and severity of harmful algal blooms (HABs) change alongside global climate, efficient tools to monitor and understand the current ecological context of these taxa are increasingly important. Here we employ environmental DNA metabarcoding to identify patterns in a wide variety of harmful algae and associated ecological communities in the Hood Canal of Puget Sound in Washington State, USA. We track trends of presence and abundance in a series of water samples across nearly two years. We find putative harmful algal sequences in a majority of samples, suggesting that these groups are routinely present in local waters. We report patterns in variants of the economically important genus Pseudo-nitzschia (family Bacillariaceae), as well as multiple harmful algal taxa previously unknown or poorly documented in the region, including a cold-water variant from the saxitoxin-producing genus Alexandrium (family Gonyaulacaceae), two variants from the karlotoxin-producing genus Karlodinium (family Kareniaceae), and one variant from the parasitic genus Hematodinium (family Syndiniaceae). We then use data on environmental variables and the biological community surrounding each algal taxon to illustrate the ecological context in which these species are commonly found. Environmental DNA metabarcoding thus simultaneously (1) alerts us to potential new or cryptic occurrences of harmful algae, (2) expands our knowledge of the co-occurring conditions and species associated with the growth of these organisms in changing marine environments, and (3) provides a tool for monitoring and management moving forward.

ecology↗

bioRxiv2019

Seagrass mediates microalgal community structure at a distance

Seagrass beds provide a variety of ecosystem services, both within and outside the bounds of the habitat itself. Here we use environmental DNA (eDNA) amplicons to analyze a broad cross-section of taxa from ecological communities in and immediately surrounding eelgrass (Zostera marina). Sampling seawater along transects extending alongshore outward from eelgrass beds, we demonstrate that eDNA provides meter-scale resolution of communities in the field. We evaluate eDNA abundance indices for thirteen major phylogenetic groups of marine and estuarine taxa along these transects, finding highly local changes linked with proximity to Z. marina for a diverse group of dinoflagellates, and for no other group of taxa. Eelgrass habitat is consistently associated with dramatic reductions in dinoflagellate abundance both within the contiguous beds and for at least fifteen meters outside, relative to nearby sites without eelgrass. These results are consistent with the hypothesis that eelgrass-associated communities have allelopathic effects on dinoflagellates, and that these effects can extend in a halo beyond the bounds of the contiguous beds. Because many dinoflagellates are capable of forming Harmful Algal Blooms (HABs) toxic to humans and other animal species, the apparent salutary effect of eelgrass habitat on neighboring waters has important implications for public health as well as shellfish aquaculture and harvesting.

ecology↗

bioRxiv2019

Understanding Environmental DNA

As environmental DNA (eDNA) studies have grown in popularity for use in ecological applications, it has become clear that their results differ in significant ways from those of traditional, non-PCR-based surveys. In general, eDNA studies that rely on amplicon sequencing may detect hundreds of species present in a sampled environment, but the resulting species composition can be idiosyncratic, reflecting species true biomass abundances poorly or not at all. Here, we use a set of simulations to develop a mechanistic understanding of the processes leading to the kinds of results common in mixed-template PCR-based (metabarcoding) studies. In particular, we focus on the effects of PCR cycle number and primer amplification efficiency on the results of diversity metrics in sequencing studies. We then show that proportional indices of amplicon reads capture trends in taxon biomass with high accuracy, particularly where amplification efficiency is high (median correlation up to 0.97). Our results explain much of the observed behavior of PCR-based studies, and lead to recommendations for best practices in the field.

molecular biology↗