Biology subjects

Zervas, A.

Publications and source records attributed to Zervas, A..

8 recordsLinked to original sources

bioRxiv2026

TriMic: a Triticum aestivum microbial culture collection and synthetic community for dissecting wheat-microbe interactions

Understanding the molecular mechanisms underlying plant-microbe interactions is essential for developing innovative microbe-based agrotechnologies. However, deciphering these mechanisms within the complexity of natural microbial communities remains challenging. Such challenges can be addressed by employing synthetic microbial communities (SynComs) derived from well characterized microbial culture collections. Despite their importance, plant-associated microbial collections from major agricultural crops remain scarce. To bridge this gap, we established TriMic, a taxonomically and functionally representative culture collection of wheat root-associated bacteria. Complementing this collection, we include high quality genome sequences and an overview of genes involved in plant colonization, nutrient cycling, and plant growth promotion. Furthermore, we expanded this experimental toolkit by designing a reduced complexity SynCom that enables controlled dissection of plant-microbe interactions. Together, these resources lay the groundwork for mechanistic studies of plant-microbe interactions to accelerate biostimulant development aimed at enhancing agricultural productivity and sustainability. The TriMic collection and whole genomes are publicly available at the DSMZ (https://www.dsmz.de/collection/catalogue/microorganisms/microbiota/trimic) and NCBI. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=166 SRC="FIGDIR/small/740170v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@91bda0org.highwire.dtl.DTLVardef@386c49org.highwire.dtl.DTLVardef@4d455aorg.highwire.dtl.DTLVardef@1043ccb_HPS_FORMAT_FIGEXP M_FIG C_FIG Overview of the workflow for development of the wheat root bacterial collection and SynCom. (a) Bacterial isolates were recovered from roots of wheat grown in natural soil using two strategies after a root slurry was prepared: directly plating or host-mediated, which involved producing a secondary root slurry from wheat roots inoculated with the original root slurry (Ben Niu et al. 2017). Both root slurries were diluted and then plated onto four different types of media (1/10 R2A, 1/20 R2A, 1/100 R2A, and VxylG). Colonies were picked based on morphology and time of appearance. (b) Non-redundant strains of 88 purified isolates were made publicly available at the German Collection of Microorganisms and Cell cultures GmbH (DSMZ). (c) A 15-species synthetic community (SynCom) was developed after evaluating community dynamics in wheat roots inoculated with a 27-member consortium selected across genera in the collection. (d) Isolate genomes were sequenced using either short-read or hybrid assemblies with long-reads. Following functional annotation, genomes were screened for traits associated with plant-microbe interactions and secondary metabolite production.

microbiology↗

bioRxiv2026

ZeaMiC: a Publicly Available Culture Collection of Maize Root-Associated Bacteria

Plant-associated microbiota are composed of hundreds of microbial species. For many of them, little is known about their individual functions and even less is known about their emergent community-level traits. While culture-independent methods provide valuable insights into the composition, diversity, and functional potential of plant-associated microbiota, culture-dependent methods are essential for reductionist lines of inquiry into the roles of individual species and their interactions within a community. Here, we present ZeaMiC, a publicly available culture collection of root-associated bacteria from Zea mays (maize). This resource comprises 88 isolates obtained from diverse soils and several maize genotypes, with live cultures available through DSMZ (German Collection of Microorganisms and Cell Cultures) both as single stocks and as cost-effective bundles (https://www.dsmz.de/collection/catalogue/microorganisms/microbiota/zeamic). To maximize relevance, isolates were selected to be representative of maize root-associated microbiomes in the Corn Belt of the United States, based on abundance-occupancy patterns from previously published root microbiome data, phylogenetic diversity, and literature-based evidence of functional importance. Whole-genome sequencing and annotation revealed genes associated with root colonization, plant growth promotion, and nutrient cycling, including functions such as chemotaxis, biofilm formation, secretion systems, hormone modulation, and phosphate solubilization. This collection serves as a community resource for future mechanistic studies of plant-microbe and microbe-microbe interactions, filling the gap in our understanding of the ecological interactions in plant microbiomes.

microbiology↗

bioRxiv2022

Abrupt permafrost thaw triggers microbial bloom and increased activity of microbial predators

Permafrost soils store a substantial part of the global soil carbon and nitrogen. However global warming causes abrupt erosion and gradual thaw, which make these stocks vulnerable to microbial decomposition into greenhouse gases. Here, we investigated the microbial response to abrupt in situ permafrost thaw. We sequenced the total RNA of a 1 m deep soil core consisting of up to 26500-year-old permafrost material from an active abrupt erosion site. We analysed the microbial community in the active layer soil, the recently thawed, and the intact permafrost and found maximum RNA:DNA ratios indicating a microbial bloom in recently thawed permafrost. Several fast-growing prokaryotic taxa dominated thawed permafrost, including Sphingobacteriales, Burkholderiales, and Nitrosomonadales. Overall, the thaw state and soil moisture consistently explained changes in community composition, with especially the permafrost community being significantly distinct from thawed soils. Predation correlated with changes in prokaryotic composition. Bacterial grazers were dominated by Myxococcales and abundant in the active layer. In contrast, protozoa, especially Cercozoa and Ciliophora, doubled in relative abundance in thawed layers. Our findings highlight the ecological importance of a rapid development of microbial blooms as well as the successive predation as biological control mechanism in abruptly thawing permafrost. One sentence summaryUsing total RNA from an up to 26500-year-old abruptly eroding permafrost site in Greenland, we described a microbial bloom and its controls, including bacterial and microeukaryotic predators. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=146 SRC="FIGDIR/small/499897v2_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@10ab79eorg.highwire.dtl.DTLVardef@9d0146org.highwire.dtl.DTLVardef@1bec509org.highwire.dtl.DTLVardef@179f397_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2021

Complete genome sequence and Benzophenone-3 mineralisation potential of Rhodococcus sp. USK10, a bacterium isolated from riverbank sediment.

Benzophenone-3 (BP3) is an organic UV filter whose presence in the aquatic environment has been linked to detrimental developmental impacts in aquatic organisms such as coral and fish. The genus Rhodococcus has been extensively studied and is known for possessing large genomes housing genes for biodegradation of a wide range of compounds, including aromatic carbons. Here, we present the genome sequence of Rhodococcus sp. USK10, which was isolated from Chinese riverbank sediment and is capable of utilising BP3 as the sole carbon source, resulting in full BP3 mineralisation. The genome consisted of 9,870,030 bp in 3 replicons, a G+C content of 67.2%, and 9,722 coding DNA sequences (CDSs). Annotation of the genome revealed that 179 of these CDSs are involved in metabolism of aromatic carbons. The complete genome of Rhodococcus sp. USK10 is the first complete, annotated genome sequence of a Benzophenone-3 degrading bacterium. Through radiolabelling, it is also the first bacterium proven to mineralise Benzophenone-3. Due to the widespread environmental prevalence of Benzophenone-3, coupled to its adverse impact on aquatic organisms, this characterisation provides an integral first step in better understanding the environmentally relevant degradation pathway of the commonly used UV filter. Given USK10s ability to completely mineralise Benzophenone-3, it could prove to be a suitable candidate for bioremediation application.

genomics↗

bioRxiv2021

Complete loss of mitochondrial complex I genes in mistletoes (Viscaceae) and evidence of polyadenylated mitochondrial transcripts shown by whole transcriptome sequencing

The profound absence of mitochondrial complex I (NADH-ubiquinone oxidoreductase) genes from the mitogenome of Viscum spp. and the rapid rates of molecular evolution characterizing most of their remaining mitochondrial genes raise questions regarding the possible transfer of the entire nad gene set to the nucleus, as well as for the functionality of the remaining highly divergent genes. Using whole transcriptome sequencing in three species of Viscaceae: V. album, V. crassulae, and Phoradendron leucarpum we were able to confirm transcription of all previously identified genes. However, we did not detect any nad gene transcripts, thus, providing further evidence of the complete loss of complex I in Viscaceae. The results from transcriptome sequencing also revealed that levels and patterns of RNA editing were not different from those found in autotrophic plant species. Hence, RNA editing is not a means of restoring conserved domains or folding sites of the proteins coded for by the divergent mitochondrial genes. Since we were able to recover mitochondrial genes transcripts following a sequencing protocol targeted towards polyadenylated mRNA molecules, it is suggested that mitochondrial genes undergo post-transcriptional polyadenylation in Viscaceae.

evolutionary biology↗

bioRxiv2020

Potential Rhodopsin and Bacteriochlorophyll-Based Dual Phototrophy in a High Arctic Glacier

Conserving additional energy from sunlight through bacteriochlorophyll (BChl)-based reaction center or proton-pumping rhodopsin is a highly successful life strategy in environmental bacteria. Rhodopsin and BChl based systems display contrasting characteristics in the size of coding operon, cost of biosynthesis, ease of expression control, and efficiency of energy production. This raises an intriguing question of whether a single bacterium has evolved the ability to perform these two types of phototrophy complementarily according to energy needs and environmental conditions. Here we report four Tardiphaga sp. strains (Alphaproteobacteria) of monophyletic origin isolated from a high Arctic glacier in northeast Greenland (81.566{degrees} N, 16.363{degrees} W) that are at different evolutionary stages concerning phototrophy. Their >99.8% identical genomes contain footprints of horizontal operon transfers (HOT) of the complete gene clusters encoding BChl and xanthorhodopsin (XR)-based dual phototrophy. Two strains only possess a complete xanthorhodopsin (XR) operon, while the other two strains have both a photosynthesis gene cluster (PGC) and an XR operon in their genomes. All XR operons are heavily surrounded by mobile genetic elements and located close to a tRNA gene, strongly signaling that a HOT event of XR operon has occurred recently. Mining public genome databases and our High Arctic glacial and soil metagenomes revealed that phylogenetically diverse bacteria have the metabolic potential of performing BChl and rhodopsin-based dual phototrophy. Our data provide new insights on how bacteria cope with the harsh and energy-deficient environments in surface glaciers, possibly by maximizing the capability of exploiting solar energy. ImportanceOver billions of years of evolution, bacteria capable of light-driven energy production have occupied every corner of surface Earth where solar irradiation can reach. Only two general biological systems have evolved in bacteria to be capable of net energy conservation via light-harvesting: one is based on the pigment of (bacterio-)chlorophyll and the other based on light-sensing retinal molecules. There is emerging genomic evidence that these two rather different systems can co-exist in a single bacterium to take advantage of their contrasting characteristics in the number of genes involved, biosynthesis cost, ease of expression control and efficiency of energy production, and thus enhance the capability of exploiting solar energy. Our data provide the first clear-cut evidence that such dual phototrophy potentially exist in glacial bacteria. Further public genome mining suggests this understudied dual phototrophic mechanism is possibly more common than our data alone suggested. Sequence data availabilityGenomes, metagenomes and raw reads were deposited into GenBank under Bioprojects PRJNA548505 and PRJNA552582.

microbiology↗

bioRxiv2019

Isolation and characterisation of novel phages infecting Lactobacillus plantarum and proposal of a new genus, \"Silenusvirus\".

Bacteria of Lactobacillus sp. are very useful to humans. However, the biology and genomic diversity of their (bacterio)phage enemies remains understudied. Knowledge on Lactobacillus phage diversity should broaden to develop efficient phage control strategies. To this end, organic waste samples were screened for phages against two wine-related Lactobacillus plantarum strains. Isolates were shotgun sequenced and compared against the phage database and each other by phylogenetics and comparative genomics. The new isolates had only three distant relatives from the database but displayed a high overall degree of genomic similarity amongst them. The latter allowed for the use of one isolate as a representative to conduct transmission electron microscopy and structural protein sequencing, and to study phage adsorption and growth kinetics. The microscopy and proteomics tests confirmed the observed diversity of the new isolates and supported their classification to the family Siphoviridae and the proposal of the new phage genus \"Silenusvirus\".

microbiology↗

bioRxiv2018

Culturomics of Aerobic Anoxygenic Phototrophic Bacteria in Wheat Phyllosphere Revealed a Divergent Evolutionary Pattern of Photosynthesis Genes in Methylobacterium spp.

The phyllosphere is a habitat to a variety of viruses, bacteria, fungi and other microorganisms, which play a fundamental role in maintaining the health of plants and mediating the interaction between plants and ambient environments. A recent addition to this catalogue of microbial diversity was the aerobic anoxygenic phototrophs (AAPs), a group of widespread bacteria that absorb light through bacteriochlorophyll (BChl a) to produce energy without fixing carbon or producing molecular oxygen. However, culture representatives of AAPs from phyllosphere and their genome information are lacking, limiting our capability to assess their potential ecological roles in this unique niche. In this study, we investigated the presence of AAPs in the phyllosphere of a winter wheat (Triticum aestivum L.) in Denmark by employing bacterial colony based infrared imaging and MALDI-TOF mass spectrometry (MS) techniques. A total of ~4480 colonies were screened for the presence of cellular BChl a, resulting in 129 AAP isolates that were further clustered into 25 groups based on MALDI-TOF MS profiling, representatives of which were sequenced using the Illumina NextSeq and Oxford Nanopore MinION platforms. Twenty draft and five complete genomes of AAPs were assembled belonging in Methylobacterium, Rhizobium, Roseomonas and a novel strain in Methylocystaceae. We observed a diverging pattern in the evolutionary rates of photosynthesis genes among the highly homogenous AAP strains of Methylobacterium (Alphaproteobacteria), highlighting an ongoing genomic innovation at the gene cluster level.

microbiology↗