Biology subjects

Ciobanu, M.

Publications and source records attributed to Ciobanu, M..

10 recordsLinked to original sources

bioRxiv2025

Earthworm invasion reduces above-belowground biodiversity and ecosystem multifunctionality

Global change alters abiotic and biotic conditions across the globe with unprecedented consequences for the functional integrity of affected ecosystems. However, most studies addressing global-change impacts focus on a very limited number of environmental variables, taxa, and ecosystem functions. Evidence is mounting that many belowground ecosystems are subject to an underappreciated aspect of global change: the invasion of earthworms. While we know that earthworm invasion can impact the physical, chemical, and biological properties of invaded ecosystems, it remains poorly understood how these changes are interconnected and how they concurrently affect the overall functioning of an ecosystem. To fill this gap, we collected data on six environmental variables, ten functional groups of microbes, plants, and animals, and 16 ecosystem functions from four forests in the USA and Canada, well-known hotspots of earthworm invasion. We used a multi-step Structural-Equation Modeling approach to disentangle the direct and indirect effects of earthworm invasion on environmental conditions and the ecosystem multidiversity and multifunctionality of invaded forests at different levels of resolution. Our analysis revealed that earthworm invasion reduced total multidiversity (combined microbial, plant, and animal multidiversity). Ecosystem multifunctionality was reduced via a combination of direct and indirect effects, with the latter involving both effects mediated by altered environmental conditions and by total multidiversity. In contrast, when resolving total multidiversity into taxon-specific multidiversity indices for microbes, plants, and animals, the above-mentioned effects of earthworm invasion on multifunctionality via multidiversity disappeared. Invasion effects on single ecosystem functions differed in their mediators but were net negative across the board. Given these differences across the differently-resolved analyses, the results suggest that a whole- ecosystem perspective is paramount to comprehensively understanding the impacts of biological invasions. Combining a multi-step analytical design with multiple biodiversity indices and multiple ecosystem functions assessed at the same time and place, our study represents the most complete assessment of the mechanisms and ecosystem-level consequences of earthworm invasion to date.

ecology↗

bioRxiv2025

Enhanced forest heterogeneity drives stronger functional than taxonomic shifts in soil nematodes

Production forests are often managed primarily for timber production, leading to biotic homogenization and reduced biodiversity. To explore strategies that promote biodiversity while maintaining timber yields, we conducted a large-scale experiment in eight German forests. We manipulated structural {beta}-complexity, i.e., the heterogeneity of structural elements across forest patches, by experimentally introducing variation in canopy gaps and different types of deadwood across 156 plots of 50 x 50 m each, to investigate its effects on forest biodiversity. We analyzed soil nematode communities, which are important bioindicators and contributors to ecosystem processes, by assessing taxonomic and functional diversity across patch (), site ({gamma}), and between-patch ({beta}) scales using Hill-Chao numbers. Additionally, we tested whether environmental variables explain nematode diversity responses. Our results show that functional diversity is more responsive than taxonomic diversity, with increased {beta}-diversity of common and frequent taxa alongside simultaneous declines in - and {gamma}-diversity. This pattern suggests a shift toward more specialized nematode communities in response to the intervention. Moreover, we found that site-specific conditions, such as sand content and understory biomass, modulated these effects. Overall, our findings reveal complex, scale-dependent responses of nematode diversity to aboveground forest structural changes, emphasizing the need to consider environmental context in forest biodiversity management. This study represents an important first step toward understanding and enhancing soil biodiversity at management-relevant spatial scales.

ecology↗

bioRxiv2024

Nucleomorph phylogenomics suggests a deep and ancient origin of cryptophyte plastids within Rhodophyta

The evolutionary origin of red algae-derived complex plastids remains obscure. Cryptophyta, one of four eukaryotic lineages harboring these plastids, still contain nucleomorphs, which are highly reduced remnants of red algal nuclei. The genes present on nucleomorph genomes can be used for phylogenomic reconstruction in order to unravel the evolutionary origin of all red complex plastids and provide data independent from previously analyzed plastid-encoded proteins. Here, we leverage these genes in a first attempt at pinpointing the position of cryptophyte nucleomorphs within a comprehensive diversity of Rhodophyta, including new sequence representatives from seven deep-branching red algae. Our analysis, supported by a series of rigorous topology tests, places cryptophyte nucleomorphs as sister to the extremophilic, freshwater subphylum Cyanidiophytina. This conflicts with previously published analyses based on plastidial genes that placed red complex plastids closer to the mesophilic Rhodophytina. Regardless of exact placement, our results reject a nucleomorph origin within any known subgroup of Rhodophyta, instead suggesting an ancient origin of complex red plastids among the deepest branches of the red algal tree of life.

microbiology↗

bioRxiv2024

Culture- and genome-based characterization of a tripartite interaction between patescibacterial epibionts, methylotrophic proteobacteria, and a jumbo phage in freshwater ecosystems

Patescibacteria form a very diverse and widely distributed phylum of small bacteria inferred to have an episymbiotic lifestyle. However, the prevalence of this lifestyle within the phylum and their host specificity remain poorly known due to the scarcity of cultured representatives. Here, we describe a complex system consisting of a patescibacterium, its gammaproteobacterial hosts, and their respective phages based on enrichment cultures and metagenomic data from two shallow, geographically close, freshwater ecosystems. The patescibacterium, Strigamonas methylophilicida sp. nov., defines a new genus within the family Absconditicoccaceae. It grows as epibiont on cells of methanotrophic species of the gammaproteobacterial family Methylophilaceae. Strigamonas cells grow tightly attached to the host, sometimes forming stacks that connect two host cells. Despite a surprisingly large genome (1.9 Mb) compared to many other Patescibacteria, S. methylophilicida lacks many essential biosynthetic pathways, including the complete biosynthesis of phospholipids, amino acids, and nucleic acids, implying a dependence on the host to obtain these molecules. We also identified and assembled the complete genomes of one patescibacterial phage that might represent a new virus family within the class Caudoviricetes, and two Methylophilaceae phages predicted to have head-tailed and filamentous virions, respectively. The patesciphage uses a modified genetic code similar to that of its host and encodes four tRNA genes, including the suppressor tRNA gene for the UGA stop codon, which is reassigned to glycine in many Patescibacteria. Our results confirm a prevalent episymbiotic lifestyle in Absconditicoccaceae and further suggest a clade-specific adaptation of this patescibacterial family for gammaproteobacterial hosts. IMPORTANCEPatescibacteria are ultra-small bacteria with reduced genomes that rely on symbiotic interactions with other prokaryotes, yet their host specificity and associated viral parasites remain poorly characterized due to limited cultured representatives. Here, we describe Strigamonas methylophilicida, a new patescibacterial species of the family Absconditicoccaceae that grows as an epibiont on various methylotrophic Gammaproteobacteria. This expands the host range for this family beyond previously documented photosynthetic partners. Using enrichment cultures and metagenomics, we retrieved complete genomes of novel phages infecting S. methylophilicida and its hosts, including one phage that uses a modified genetic code matching that of the patescibacterium. These findings reveal a previously unrecognized patescibacteria- methylotroph-phage tripartite interaction in freshwater environments, highlight the adaptations of patescibacterial phages, and shed light on the complex ecology and evolution of host-parasite-phage dynamics in understudied bacterial lineages.

microbiology↗

bioRxiv2023

Sustainable land management enhances ecological and economic multifunctionality under ambient and future climate

1.Anthropogenic activity is threatening ecosystem multifunctionality, i.e. the ability of ecosystems to provide multiple functions and services which are vital for human well-being. Here we assess how multifunctionality of agroecosystems in Central Germany depends on land-use type and climate change. Our analysis included 13 ecosystem functions in a large-scale field experiment with five different land-use types (three grassland and two farmland types either sustainably or intensively managed) under two different climate scenarios (ambient and future climate). We consider ecological measures of multifunctionality using averaging approaches with different weights, i.a. reflecting preferences of farmers and environmentalists, and assess an economic multifunctionality measure based on the total value of ecosystem services. Results show that intensive management and future climate decrease ecological multifunctionality for multiple weighting scenarios in both grassland and farmland. Only under a weighting according to farmers preferences, intensively-managed grassland shows higher multifunctionality as compared to sustainably-managed grassland. The economic multifunctionality measure, which includes economic benefits for society at large, reveals a multifunctionality about [~]1.7 times higher for sustainable compared to intensive management for both grassland and farmland. Above-belowground biodiversity correlates positively with ecosystem multifunctionality and is expected to be one of its main drivers. Based on these findings, we suggest to promote and economically incentivise sustainable land management that enhances both ecological and economic multifunctionality, also under future climatic conditions.

ecology↗

bioRxiv2022

Expanding the molecular and morphological diversity of Apusomonadida, a deep-branching group of gliding bacterivorous protists

Apusomonads are cosmopolitan bacterivorous biflagellate protists usually gliding on freshwater and marine sediment or wet soils. These nanoflagellates form a sister lineage to opisthokonts and may have retained ancestral features helpful to understanding the early evolution of this large supergroup. Although molecular environmental analyses indicate that apusomonads are genetically diverse, few species have been described. Here, we morphologically characterize eleven new apusomonad strains. Based on molecular phylogenetic analyses of the rRNA gene operon, we describe four new strains of the known species Multimonas media, Podomonas capensis, Apusomonas proboscidea and Apusomonas australiensis, and rename Thecamonas oxoniensis as Mylnikovia oxoniensis n. gen., n. comb. Additionally, we describe four new genera and six new species: Catacumbia lutetiensis n. gen. n. sp., Cavaliersmithia chaoae n. gen. n. sp., Singekia montserratensis n. gen. n. sp., Singekia franciliensis n. gen. n. sp., Karpovia croatica n. gen. n. sp. and Chelonemonas dolani n. sp. Our comparative analysis suggests that apusomonad ancestor was a fusiform biflagellate with a dorsal pellicle, a plastic ventral surface and a sleeve covering the anterior flagellum, that thrived in marine, possibly oxygen-poor, environments. It likely had a complex cell cycle with dormant and multiple fission stages, and sex. Our results extend known apusomonad diversity, allow updating their taxonomy, and provide elements to understand early eukaryotic evolution.

microbiology↗

bioRxiv2022

Description of Gloeomargarita ahousahtiae sp. nov., a thermophilic member of the order Gloeomargaritales with intracellular carbonate inclusions

A unicellular cyanobacterium, strain VI4D9, was isolated from thermophilic microbial mats thriving in a hot spring of the Ahousaht territory of Vancouver Island, Canada. The cells were elongated rods (5.1 m in length and 1.2 m in width on average). Their UV-visible absorption spectra revealed that they contain chlorophyll a, phycocyanin, and carotenoids. Transmission electron microscopy showed the presence of thylakoids concentrated on one side of the cells. The strain grew within a temperature range of 37-50{degrees}C, with an optimum at 45{degrees}C. Its genome had a size of 3,049,282 bp and a DNA G+C content of 51.8 mol%. The cells contained numerous intracellular spherical granules easily visible under scanning electron microscopy. Energy-dispersive x-ray spectroscopy revealed that these granules were made of Ca-, Ba- and Sr-containing carbonates. A phylogenetic 16S rRNA gene tree robustly placed this strain as sister to several environmental sequences and the described species Gloeomargarita lithophora, also characterized by the possession of intracellular carbonate inclusions. We consider strain VI4D9 to represent a new Gloeomargarita species based on its marked phenotypic differences with G. lithophora, notably, its thermophilic nature and different thylakoid organization. We propose the name Gloeomargarita ahousahtiae sp. nov. for this newly isolated thermophilic cyanobacterium. The type strain is VI4D9 (Culture Collection of Algae and Protozoa strain 1472/1; Laboratorio de Algas Continentales Mexico strain LAC 140). G. ahousahtiae is the second species described within the recently discovered order Gloeomargaritales.

microbiology↗

bioRxiv2021

Viral and parasitic cell ratios per free-living microbe across ecosystems

It is generally assumed that viruses outnumber cells on Earth by at least tenfold. Virus-to-microbe ratios (VMR) are largely based on counts of fluorescently labelled virus-like particles. However, these exclude intracellular viruses and potentially include false positives (DNA-containing vesicles, gene-transfer agents, unspecifically stained inert particles). Here, we develop a metagenome-based VMR estimate (mVRM) that accounts for DNA viruses across all stages of their replication cycles (virion, intracellular lytic and lysogenic) by using normalised RPKM (reads per kilobase of gene sequence per million of mapped metagenome reads) counts of the major capsid protein (MCP) genes and cellular universal single-copy genes (USCGs) as proxies for virus and cell counts, respectively. After benchmarking this strategy using mock metagenomes with increasing VMR, we inferred mVMR across different biomes. To properly estimate mVMR in aquatic ecosystems, we generated metagenomes from co-occurring cellular and viral fractions (>50 kDa-200 {micro}m size-range) in freshwater, seawater and solar saltern ponds (10 metagenomes, 2 control metaviromes). Viruses outnumbered cells in freshwater by [~]13 fold and in plankton from marine and saline waters by [~]2-4 fold. However, across an additional set of 121 diverse non-aquatic metagenomes including microbial mats, microbialites, soils, freshwater and marine sediments and metazoan-associated microbiomes, viruses, on average, outnumbered cells by barely two-fold. Although viruses likely are the most diverse biological entities on Earth, their global numbers might be closer to those of cells than previously estimated.

microbiology↗

bioRxiv2018

Diversity-dependent plant-soil feedbacks underlie long-term plant diversity effects on primary productivity

Although diversity-dependent plant-soil feedbacks (PSFs) may contribute significantly to plant diversity effects on ecosystem functioning, the influence of underlying abiotic and biotic mechanistic pathways have been little explored to date. Here, we assessed such pathways with a PSF experiment using soil conditioned for [≥]12 years from two grassland biodiversity experiments. Model plant communities differing in diversity were grown in soils conditioned by plant communities with either low- or high-diversity (soil history). Our results reveal that plant diversity can modify plant productivity through both diversity-mediated plant-plant and plant-soil interactions, with the main driver (current plant diversity or soil history) differing with experimental context. The underlying mechanisms of PSFs were explained to a significant extent by both abiotic and biotic pathways (specifically, nematode richness and soil nitrogen availability). Thus, effects of plant diversity loss on ecosystem functioning may persist or even increase over time because of biotic and abiotic soil legacy effects.

ecology↗

bioRxiv2018

The effects of drought and nutrient addition on soil organisms vary across taxonomic groups, but are constant across seasons

Anthropogenic global change alters the activity and functional composition of soil communities that are responsible for crucial ecosystem functions and services. Two of the most pervasive global change drivers are drought and nutrient enrichment. However, the responses of soil organisms to interacting global change drivers remain widely unknown. We tested the interactive effects of extreme drought and fertilization on soil biota ranging from microbes to invertebrates across seasons. We expected drought to reduce the activity of soil organisms and fertilization to induce positive bottom-up effects via increased plant productivity. Furthermore, we hypothesized fertilization to reinforce drought effects through enhanced plant growth, resulting in even dryer soil conditions. Our results revealed that drought had detrimental effects on soil invertebrate feeding activity and simplified nematode community structure, whereas soil microbial activity and biomass were unaffected. Microbial biomass increased in response to fertilization, whereas invertebrate feeding activity substantially declined. Notably, these effects were consistent across seasons. The dissimilar responses suggest that soil biota differ vastly in their vulnerability to global change drivers. As decomposition and nutrient cycling are driven by the interdependent concurrence of microbial and faunal activity, this may imply far-reaching consequences for crucial ecosystem processes in a changing world.

ecology↗