Biology subjects

Lanzen, A.

Publications and source records attributed to Lanzen, A..

10 recordsLinked to original sources

bioRxiv2026

Microbial ecological insights from estuarine sediments revealed by temporal and spatial network analysis

Association network analyses performed on microbial abundance data provides information regarding ecosystems functioning, quality and potential keystone taxa. Samples for network analyses can be collected spatially, temporally or both. Here, we compare the microbiomes and the reconstructed association networks resulting from temporal vs spatial sampling regimes from the Oka estuary in the Spanish Basque Country. The taxonomic composition although similar at Phylum level, diverged more at lower taxonomic levels such as Family. The dissimilarity of spatial replicates was higher than the temporal replicates; however, the dispersion of OTU abundances across samples was similar in the two datasets, indicating that OTU abundances varied similarly across samples. Moreover, the topological properties and keystones differed between networks. The number of edges and the connectance were higher in the spatial network, and keystones were more taxonomically diverse in the temporal network. Among those correlations present in the spatial and temporal networks, we identified potential interactions involved in the sulphur and nitrogen cycles, and in the degradation of organic matter. We conclude that network analyses reveal ecological aspects of the ecosystems functioning, nevertheless, the sampling must be thoroughly planned according to the aim of the study, since different sampling strategies may result in different outcomes.

ecology↗

bioRxiv2026

Taxonomic vs. Functional Diversity for the Impact Assessment of Offshore Oil & Gas Activities: An Exploratory Study on Benthic Prokaryotes

Improving environmental management in the offshore Oil & Gas sector requires approaches that capture the ecosystem services (ES) provided by marine sediments, particularly their roles in carbon and nutrient cycling. Microbial communities are central to these processes, and molecular tools offer new opportunities to assess their functional diversity. To explore how different sequencing approaches inform environmental impact assessment, we compared taxonomic and functional prediction based on 16S metabarcoding, shotgun metagenomics and messenger RNA-based metatranscriptomics, targeting prokaryotic communities. Our aims were to evaluate the ability of each approach to detect impact and to determine how well they captured functions relevant to ES. All approaches revealed clear differences in community composition between impacted and non-impacted sediments at both taxonomic and functional levels, with impact significantly associated with hydrocarbon and barium content. Functional inventories showed substantial overlap across the three approaches, and 48-55 ES-related processes were detectable in all datasets. While metagenomics provided the strongest statistical discrimination between impact groups, metatranscriptomics resolved the actively expressed pathways underpinning ES, yielding the most biologically meaningful functional profiles despite its lower statistical power. All approaches indicated that Oil & Gas activity drives shift towards anaerobic, hydrocarbon-degrading, and sulfur-respiring microbial communities, with hydrocarbon degradation, sulfur cycling, and metal detoxification being the dominant ES processes in impacted sediments. Metabarcoding was confirmed as a cost-effective option for impact assessment when focused on taxonomic composition. However, functional prediction from metabarcoding data proved less reliable, as several ES showed contrasting associations to impact category between metabarcoding and shotgun sequencing approaches.

microbiology↗

bioRxiv2026

Is DNA metabarcoding an option for formaldehyde-preserved zooplankton time series?

The recovery of amplifiable DNA from formaldehyde{square}fixed (FF) zooplankton samples has long been considered unfeasible. Nevertheless, advances in DNA sequencing and methods for retrieving highly degraded genetic material have demonstrated that even million{square}year{square}old samples and FF museum specimens can yield usable DNA. To access the biological information preserved in long{square}term zooplankton time series, we assessed methodologies for extracting amplifiable DNA from community samples stored for up to 28 years in formaldehyde at room temperature. On one hand, we report the failure of a method previously described as successful for FF zooplankton samples, likely due to the cold{square}storage conditions (4{square}{degrees}C) used in the original study. On the other hand, by adapting two extraction protocols designed for FF museum specimens--representing harsher and softer alternatives (HHA and HPC, respectively)--we successfully amplified and sequenced a subset of FF zooplankton samples. As expected, DNA integrity and sample pH were inversely related to preservation time, and only short DNA fragments were recovered, ruling out the use of commonly employed [≥]300{square}bp metabarcoding markers. While DNA integrity appeared to be a better predictor than DNA yield for amplification success, the presence of a gel band of the expected size did not always guarantee congruence with microscopy{square}based assessments. Although amplifiable DNA was recovered from most samples, including some of the oldest, community compositions concordant with microscopy were consistently recovered only from samples preserved for up to two years. Beyond this point, the HHA and HPC methods produced divergent results, reflecting a trade{square}off between the removal of formaldehyde{square}induced cross{square}linkages and the avoidance of additional DNA damage. Among the small universal markers tested ([~]120-170{square}bp), including one nuclear rRNA marker and two mitochondrial markers, only the 18S rRNA V9 region consistently amplified. We conclude by providing a set of recommendations aimed at improving the methods presented here.

zoology↗

bioRxiv2025

Benchmarking beta-diversity measures and transfer functions for sedimentary ancient DNA

Analyzing past ecosystems can improve our understanding of the mechanisms linking biodiversity with environmental changes. Sedimentary ancient DNA (sedaDNA) opens a window to past biodiversity, beyond the fossil record, that can be used to reconstruct ancient environments and ecosystems functions. To this end, modern biodiversity and environmental conditions are used to calibrate transfer functions, that are then applied to past biodiversity data to reconstruct environmental parameters. Doing this with sedaDNA can be challenging, because ancient DNA is often obtained in limited quantities and fragmented into smaller molecules. This leads to noisy datasets, with a low alpha diversity relative to modern DNA, patchy taxa detection patterns and/or skewed relative abundance profiles. How this affects beta-diversity measures, and the performance of transfer functions remain untested. Here we simulated ancient DNA reads counts matrices from synthetic and empirical datasets, and tested 464 combinations of counts transformations, beta-diversity indices, and ordinations methods, and assessed their performance in i) separating the ecological signal from the noise introduced by DNA degradation and in ii) predicting ground-truth environmental conditions. Our results show that commonly used workflows in DNA-based community ecology studies are sensitive to the noise associated to ancient DNA signal. Instead, combinations of methods that include more recent ordination methods proved robust to ancient DNA noise and produced better transfer functions. Our study provides a framework for designing post-processing workflows that are better suited for sedaDNA studies.

ecology↗

bioRxiv2025

Contrasting dynamics and biotic association networks in estuarine microbenthic communities along an environmental disturbance gradient

Estuarine ecosystems experience a range of anthropogenic pressures. Consequently, robust monitoring tools are essential for their management and protection. Utilising environmental DNA in routine monitoring programs enables the inclusion of benthic microorganisms, which are not only good indicators of environmental condition, but also play critical roles in ecosystem functioning. In this study we collect eDNA from sediment samples across time in six estuaries, from the Basque coast (Spain), under varying degrees of disturbance. To identify potential indicators of biotic integrity (environmental health status), we used time series data to examine the prokaryotic microbial communities and consensus networks associated with different levels of pollution. In general, sediment communities were relatively temporally stable, with the moderately and heavily disturbed sites showing more variation. The consensus networks also differed significantly in their topologies, with more impacted estuaries having fewer nodes, edges and connectance, among others, and higher modularity compared to those less impacted. Moreover, the potential keystone taxa and predicted functional profiles differed between consensus networks. This illustrates how modelled association networks can reveal new insights regarding the state of estuarine ecosystems and their potential functional processes.

ecology↗

bioRxiv2023

Increasing marine trophic web knowledge through DNA analyses of fish stomach contents: a step towards an Ecosystem Based Approach to fisheries research

Multispecies and ecosystem models, which are key for the implementation of ecosystem-based approaches to fisheries management, require extensive data on the trophic interactions between marine organisms, including changes over time. DNA metabarcoding (the simultaneous identification of all taxa in a sample by sequencing a short DNA region) could be used for speeding up large-scaled stomach content data collection. Yet, for DNA metabarcoding to be routinely implemented, technical challenges should be addressed, such as the potentially complicated sampling logistics, the detection of a high proportion of predator DNA, and the inability to provide reliable abundance estimations. Here, we present a DNA metabarcoding assay developed to examine the diet of five commercially important fish, which is feasible to be incorporated into routinary samplings. The method is devised to speed up the analysis process by avoiding the stomach dissection and content extraction steps, while preventing the amplification of predator DNA by using blocking primers. Tested in mock samples and in real stomachs, the method has proven effective and shows great effectiveness discerning diet variations due to predator ecology or prey availability. Additionally, by applying our protocol to mackerel stomachs previously analysed by visual inspection, we showcase how DNA metabarcoding could complement visually based data by detecting overlooked prey by the visual approach. We finally discuss how DNA metabarcoding-based data can contribute to trophic data collection. Our work reinforces the potential of DNA metabarcoding for the study and monitoring of fish trophic interactions and provides a basis for its incorporation into routine monitoring programs, which will be critical for the implementation of ecosystem-based approaches to fisheries management.

ecology↗

bioRxiv2023

Diversity and biotechnological potential of filamentous fungi isolated from sediments of Basque estuaries

Marine environments harbor a vast diversity of microorganisms, which have developed multiple strategies to adapt to challenging conditions and represent a valuable source for new products such as pigments, enzymes and bioactive compounds. From all microorganisms inhabiting marine environments, fungi have been the least studied, despite their ubiquitous presence and great biotechnological potential. Here, we focused on the isolation and characterization of filamentous fungi from marine sediment samples, which were collected along the Basque coast in Spain. Through phenotypic characterization, we identified isolates potentially able to produce secondary metabolites or grow on minimal culture medium supplemented with recalcitrant algal polysaccharides. Based on this screening, two Sordariomycetes isolates were selected for further analyses through genome sequencing and omics techniques: 1) a Marquandomyces marquandii strain able to stain the culture medium in yellow, indicative of secretion of pigments and secondary metabolites and 2) an Albophoma yamanashiensis strain able to grow in minimal culture medium supplemented with the recalcitrant algal polysaccharide fucoidan. Fungal co-culture experiments suggested an inhibitory effect of the secretome of M. marquandii on fungal growth. Under culture conditions inducing pigment secretion, a set of secondary metabolite gene clusters were differentially expressed, as analysed by RNA-seq. On the other hand, transcriptomic and proteomic experiments on A. yamanashiensis unveiled the enzymatic activities expressed in response to the presence of fucoidan. Overall, our results indicate that the isolated marine fungal strains could serve as a source of new enzymatic activities and secondary metabolites.

microbiology↗

bioRxiv2020

Cropping systems that improve richness convey increased resistance and resilience to fungal, but not prokaryote, communities.

Crop harvest followed by a fallow period can act as a disturbance on soil microbial communities. Cropping systems intended to improve alpha-diversity of communities may also confer increased compositional stability during succeeding growing seasons. Over a single growing season in a long-term (18 year) agricultural field experiment incorporating conventional (CON), conservation (CA), organic (ORG) and integrated (INT) cropping systems, temporal changes in prokaryote, fungal and arbuscular mycorrhizal fungi (AMF) communities were investigated overwinter, during crop growth and at harvest. While certain prokaryote phyla were influenced by cropping system (e.g. Acidobacteria), the community as a whole was primarily driven by temporal changes over the growing season as distinct overwinter and crop-associated communities, with the same trend observed regardless of cropping system. Species- rich prokaryote communities were most stable over the growing season. Cropping system exerted a greater effect on fungal communities, with alpha-diversity highest and temporal changes most stable under CA. CON was particularly detrimental for alpha-diversity in AMF communities, with AMF alpha-diversity and stability improved under all other cropping systems. Practices that promoted alpha-diversity tended to also increase the similarity and temporal stability of soil fungal (and AMF) communities during a growing season, while prokaryote communities were largely insensitive to management.

microbiology↗

bioRxiv2019

To assemble or not to resemble -- A validated Comparative Metatranscriptomics Workflow (CoMW)

BackgroundMetatranscriptomics has been used widely for investigation and quantification of microbial communities activity in response to external stimuli. By assessing the genes expressed, metatranscriptomics provide an understanding of the interactions between different major functional guilds and the environment. Here, we present de-novo assembly-based Comparative Metatranscriptomics Workflow (CoMW) implemented in a modular, reproducible structure, significantly improving the annotation and quantification of metatranscriptomes. Metatranscriptomics typically utilize short sequence reads, which can either be directly aligned to external reference databases (\"assembly-free approach\") or first assembled into contigs before alignment (\"assembly-based approach\"). We also compare CoMW (assembly-based implementation) with assembly-free alternative workflow, using simulated and real-world metatranscriptomes from Arctic and Temperate terrestrial environments. We evaluate their accuracy in precision and recall using generic and specialized hierarchical protein databases.\n\nResultsCoMW provided significantly fewer false positives resulting in more precise identification and quantification of functional genes in metatranscriptomes. Using the comprehensive database M5nr, the assembly-based approach identified genes with only 0.6% false positives at thresholds ranging from inclusive to stringent compared to the assembly-free approach yielding up to 15% false positives. Using specialized databases (Carbohydrate Active-enzyme and Nitrogen Cycle), the assembly-based approach identified and quantified genes with 3-5x less false positives. We also evaluated the impact of both approaches on real-world datasets.\n\nConclusionsWe present an open source de-novo assembly-based Comparative Metatranscriptomics Workflow (CoMW). Our benchmarking findings support the argument of assembling short reads into contigs before alignment to a reference database, since this provides higher precision and minimizes false positives.

bioinformatics↗

bioRxiv2019

Total RNA-sequencing reveals multi-level microbial community changes and functional responses to wood ash application in agricultural and forest soil

Recycling of wood ash from energy production may counteract soil acidification and return essential nutrients to soils. However, wood ash amendment affects soil physicochemical parameters that control composition and functional expression of the soil microbial community. Here, we applied Total RNA-sequencing to simultaneously assess the impact of wood ash amendment on the active soil microbial communities and the expression of functional genes from all microbial taxa. Wood ash significantly affected the taxonomic (rRNA) as well as functional (mRNA) profiles of both agricultural and forest soil. Increase in pH, electrical conductivity, dissolved organic carbon and phosphate were the most important physicochemical drivers for the observed changes. Wood ash amendment increased the relative abundance of the copiotrophic groups Chitinonophagaceae (Bacteroidetes) and Rhizobiales (Alphaproteobacteria) and resulted in higher expression of genes involved in metabolism and cell growth. Finally, Total RNA-sequencing allowed us to show that some groups of bacterial feeding protozoa increased concomitantly to the enhanced bacterial growth, which shows their pivotal role in the regulation of bacterial abundance in soil.

microbiology↗