Biology subjects

Tikhonenkov, D. V.

Publications and source records attributed to Tikhonenkov, D. V..

7 recordsLinked to original sources

bioRxiv2024

Temporal Dynamics and Adaptive Mechanisms of Microbial Communities: Divergent Responses and Network Interactions

Microbial communities are integral to aquatic ecosystems, playing key roles in biogeochemical cycles, nutrient recycling, and ecosystem functioning. Despite their importance, the temporal dynamics of these communities, especially in response to short-term environmental changes, remain inadequately understood. This study utilizes high-throughput amplicon sequencing and Co-occurrence network analysis to elucidate how prokaryotic and eukaryotic microbial communities dynamically respond to short-term environmental fluctuations, and dynamics of networks. Our results reveal distinct temporal patterns, with eukaryotic communities showing consistent increases in diversity, while prokaryotic communities exhibited more pronounced fluctuations and directional changes. Co-occurrence network analysis further highlighted the differences in community structure between phases of homogenization and heterogenization. Specifically, we observed a shift from a more modular network during the homogenization phase to a more centralized network in the heterogenization phase, resulting in increased network fragility. Environmental factors, such as nutrient levels and climatic conditions, were found to play pivotal roles in shaping these dynamics. This study provides critical insights into the resilience and adaptability of microbial communities, emphasizing the intricate interplay between biodiversity, network structure, and ecosystem stability under varying environmental conditions.

microbiology↗

bioRxiv2021

Monophyly of Diverse Bigyromonadea and their Impact on Phylogenomic Relationships Within Stramenopiles

Stramenopiles are a diverse but relatively well-studied eukaryotic supergroup with considerable genomic information available (Sibbald and Archibald, 2017). Nevertheless, the relationships between major stramenopile subgroups remain unresolved, in part due to a lack of data from small nanoflagellates that make up a lot of the genetic diversity of the group. This is most obvious in Bigyromonadea, which is one of four major stramenopile subgroups but represented by a single transcriptome. To examine the diversity of Bigyromonadea and how the lack of data affects the tree, we generated transcriptomes from seven novel bigyromonada species described in this study: Develocauda condao, Develocanicus komovi, Develocanicus vyazemskyi, Cubaremonas variflagellatum, Pirsonia chemainus, Feodosia pseudopoda, and Koktebelia satura. Both maximum likelihood and Bayesian phylogenomic trees based on a 247 gene-matrix recovered a monophyletic Bigyromonadea that includes two diverse subgroups, Developea and Pirsoniales, that were not previously related based on single gene trees. Maximum likelihood analyses show Bigyromonadea related to oomycetes, whereas Bayesian analyses and topology testing were inconclusive. We observed similarities between the novel bigyromonad species and motile zoospores of oomycetes in morphology and the ability to self- aggregate. Rare formation of pseudopods and fused cells were also observed, traits that are also found in members of labyrinthulomycetes, another osmotrophic stramenopiles. Furthermore, we report the first case of eukaryovory in the flagellated stages of Pirsoniales. These analyses reveal new diversity of Bigyromonadea, and altogether suggest their monophyly with oomycetes, collectively known as Pseudofungi, is the most likely topology of the stramenopile tree.

evolutionary biology↗

bioRxiv2020

Heterotrophic flagellates and centrohelid heliozoans from marine waters of Curacao, the Netherlands Antilles

Recent progress in understanding the early evolution of eukaryotes was tied to morphological identification of flagellates and heliozoans in the natural samples, isolation of their cultures and genomic and ultrastructural investigations. These protists are the smallest and least studied microbial eukaryotes but play an important role in functioning of microbial food webs. Using light and electron microscopy, we have studied the diversity of heterotrophic flagellates and centrohelid heliozoans from marine waters of Curacao (The Netherlands Antilles), and provide micrographs and morphological descriptions of observed species. Among 86 flagellates and 3 centrohelids encountered in this survey, five heterotrophic flagellates and one Centrohelid heliozoan were not identified even to the genus. Some flagellate protists have a unique morphology, and may represent undescribed lineages of eukaryotes of high taxonomic rank. The vast majority (89%) of identified flagellates are characterized by wide geographical distribution and had been reported previously from all hemispheres and various climatic regions. More than half of the species were previously observed not only from marine, but also from freshwater habitats. The parameters of the species accumulation curve indicate that our species list obtained for the Curacao study sites is far from complete, and each new sample should yield new species.

microbiology↗

bioRxiv2020

Predatory colponemids are the sister group to all other alveolates

Alveolates are a major supergroup of eukaryotes encompassing more than ten thousand free-living and parasitic species, including medically, ecologically, and economically important apicomplexans, dinoflagellates, and ciliates. These three groups are among the most widespread eukaryotes on Earth, and their environmental success can be linked to unique innovations that emerged early in each group. Understanding the emergence of these well-studied and diverse groups and their innovations has relied heavily on the discovery and characterization of early-branching relatives, which allow ancestral states to be inferred with much greater confidence. Here we report the phylogenomic analyses of 313 eukaryote protein-coding genes from transcriptomes of three members of one such group, the colponemids (Colponemidia), which unambiguously support their monophyly and position as the sister lineage to all other alveolates. Colponemid-related sequences from environmental surveys and our microscopical observations show that colponemids are not common in nature, but diverse and widespread in freshwater habitats around the world. Studied colponemids possess two types of extrusive organelles (trichocysts or toxicysts) for active hunting of other unicellular eukaryotes and potentially play an important role in microbial food webs. Colponemids have generally plesiomorphic morphology and illustrate the ancestral state of Alveolata. We further discuss their importance in understanding the evolution of alveolates as well as origin of myzocytosis and plastids. HighlightsO_LIPhylogenomics resolves Colponemidia as a sister group to all other alveolates C_LIO_LIThe ancestor of all alveolates was a biflagellate predator feeding by phagocytosis C_LIO_LIColponemids may illuminate the ancestral states of apicomplexans, dinoflagellates, and ciliates C_LIO_LIColponemids are geographically widespread in freshwater habitats C_LI

evolutionary biology↗

bioRxiv2019

Insights into the origin of metazoan multicellularity from predatory unicellular relatives of animals

The diversity and biology of unicellular relatives of animals has strongly informed our understanding of the transition from single-celled organisms to the multicellular Metazoa. Here we analyse the cellular structures and complex life cycles of the novel unicellular holozoans Pigoraptor and Syssomonas (Opisthokonta). Both lineages are characterized by complex life cycles with a variety of cell types, the formation of multicellular aggregations and syncytium-like structures, and an unusual diet for single-celled opisthokonts (partial cell fusion and joint sucking of a large eukaryotic prey), all of which provide new insights into the origin of multicellularity in Metazoa. The ability to feed on large eukaryotic prey could have been a powerful trigger in the formation and development both aggregative (e.g., joint feeding, which also implies signalling) and clonal (e.g., hypertrophic growth followed by palintomy) multicellular stages that played important roles in the emergence of multicellular animals.

evolutionary biology↗

bioRxiv2019

Ecological and evolutionary patterns in the enigmatic protist genus Percolomonas (Heterolobosea; Discoba) from diverse habitats

The heterotrophic flagellate Percolomonas cosmopolitus (Heterolobosea) is often observed in saline habitats worldwide that range from coastal waters to saturated brines. However, only two cultures assigned to this morphospecies have been examined using molecular methods, and their 18S rRNA gene sequences are extremely different. Further the salinity tolerances of individual strains are unknown. Thus, our knowledge on the autecology and diversity in this morphospecies is deficient. Here, we report 18S rRNA gene data on seven strains similar to P. cosmopolitus from seven geographically remote locations (New Zealand, Kenya, Korea, Poland, Russia, Spain, and the USA) with sample salinities ranging from 4{per thousand} to 280{per thousand}, and compare morphology and salinity tolerance of the nine available strains. Percolomonas cosmopolitus-like strains show few-to-no consistent morphological differences, and form six clades separated by often extremely large 18S rDNA divergences (up to 42.4%). Some strains grew best at salinities from 75 to 125{per thousand} and represent halophiles. All but one of these belonged to two geographically heterogeneous clusters that formed a robust monophyletic group in phylogenetic trees; this likely represents an ecologically specialized subclade of halophiles. Our results suggest that P. cosmopolitus is a cluster of several cryptic species (at least), which are unlikely to be distinguished by geography. Interestingly, the 9 Percolomonas strains formed a clade in 18S rDNA phylogenies, unlike most previous analyses based on two sequences.

microbiology↗

bioRxiv2018

New phylogenomic analysis of the enigmatic phylum Telonemia further resolves the eukaryote tree of life

The broad-scale tree of eukaryotes is constantly improving, but the evolutionary origin of several major groups remains unknown. Resolving the phylogenetic position of these orphan groups is important, especially those that originated early in evolution, because they represent missing evolutionary links between established groups. Telonemia is one such orphan taxon for which little is known. The group is composed of molecularly diverse biflagellated protists, often prevalent although not abundant in aquatic environments. Telonemia has been hypothesized to represent a deeply diverging eukaryotic phylum but no consensus exists as to where it is placed in the tree. Here, we established cultures and report the phylogenomic analyses of three new transcriptome datasets for divergent telonemid lineages. All our phylogenetic reconstructions, based on 248 genes and using site-heterogeneous mixture models, robustly resolve the evolutionary origin of Telonemia as sister to the Sar supergroup. This grouping remains well supported when as few as 60% of the genes are randomly subsampled, thus is not sensitive to the sets of genes used but requires a minimal alignment length to recover enough phylogenetic signal. Telonemia occupies a crucial position in the tree to examine the origin of Sar, one of the most lineage-rich eukaryote supergroups. We propose the moniker TSAR to accommodate this new mega-assemblage in the phylogeny of eukaryotes.

evolutionary biology↗