Biology subjects

Vazquez-Campos, X.

Publications and source records attributed to Vazquez-Campos, X..

9 recordsLinked to original sources

bioRxiv2026

Characterisation and genomic analysis of bacterial nutritional endosymbionts in Australian ticks from shotgun metagenomic sequencing

Ticks are obligate hematophagous arthropods and feed exclusively on blood. As blood is nutrient-poor, ticks rely on bacterial endosymbionts to synthesise nutrients, yet the diversity and functional roles of these symbionts in Australian ticks remain largely uncharacterised. This is critical to address as these ticks are of high medical importance in Australia. In this study, shotgun metagenomic sequencing was performed on Bothriocroton concolor, Bothriocroton hydrosauri, Haemaphysalis longicornis and Ixodes holocyclus, enabling the recovery of six complete or partial metagenome-assembled genomes (MAGs). These comprised Coxiella-like endosymbionts (CLE), a facultative Rickettsia symbiont, and two Midichloria mitochondrii strains (Ixholo1 and Ixholo2). Functional annotation of these taxon-specific symbionts revealed the absence of virulence factors and the presence of B-vitamin and/or heme biosynthesis genes, indicative of nutritional mutualism, which is essential for tick hematophagy. The CLEs additionally harbour genes of the shikimate pathway, which modulate blood feeding in ticks by regulating serotonin biosynthesis. Furthermore, functional annotation and pangenomic analysis of Midichloria spp. found evidence that the genus may encompass multiple species, as well as the retention of genes potentially associated with an intramitochondrial lifestyle in M. mitochondrii Ixholo2. Tick microbiomes are dominated by non-pathogenic microorganisms, which are often overshadowed by pathogens. These include the endosymbionts, which can influence host biology and pathogen transmission, and are fundamental for the development of diagnostic tools and taxon-specific tick biocontrols.

microbiology↗

bioRxiv2026

Viruses, Proviruses and Satellites from Asgard Archaea Enrichments Reveal Complex Microbial Interactions

Asgard archaea are the closest known relatives of eukaryotes and are central to models of eukaryogenesis involving archaeal bacterial symbiosis, yet the contribution of viruses remains unexplored. Here, for the first time, we visualised unique viruses associated with Asgard archaeal cells. Additionally, we identified the first putative Asgard-archaeal virus satellite, which exhibited genomic interactions involving a bacterium, Stromatodesulfovibrio nilemahensis, providing evidence of a virus-mediated interaction between an Asgard archaeon and a bacterium. Additionally, novel proviruses of S. nilemahensis displayed distinct genomic features where predictions of alternate recombination sites suggested the acquisition of horizontally acquired genes associated with biofilm formation. Further, we comprehensively characterise (pro)viruses associated with this co-culture using high resolution cryo-electron tomography, proximity ligation (Hi-C), and metagenomics. Together, these findings expand the known diversity of Asgard archaeal viruses and establish a foundation for investigating the role of viruses in microbial symbiosis relevant to the emergence of eukaryotic life.

microbiology↗

bioRxiv2026

The origin and evolution of archaeal Borg extrachromosomal elements

Borgs are giant linear extrachromosomal elements (ECEs) of methane-oxidizing Methanoperedens archaea whose evolutionary origin and ecosystem distribution remain unknown. Here we detected 240 Borgs in diverse saline, soil, and freshwater ecosystems. 27 encode methyl-coenzyme M reductases central to methane metabolism, eight have full rRNA operons related to those of Methanoperedens, and some contain up to four ribosomal proteins. We also identified 323 mini-Borgs whose proteome content and gene phylogenies classify as a distinct ECE type. Based on 105 complete and near-complete genomes, Borgs and mini-Borgs share core genes in conserved order, indicating common ancestry. Phylogenetic and diversity analyses suggest that Borgs evolved via gene acquisition into a backbone inherited from mini-Borgs. This evolutionary trajectory mirrors those proposed for giant viruses of both eukaryotes and bacteria.

microbiology↗

bioRxiv2026

Trace gas oxidation supports sub-surface microbial communities across Namib Desert fog and aridity gradients

Widely accepted climate predictions indicate that drylands will expand to cover more than half of the Earths terrestrial surface by the end of the 21st century. In these environments, harsh conditions including nutrient and water limitations restrict plant and animal life, thereby increasing the importance of soil microbial communities in nutrient cycling and ecosystem functioning. The Namib Desert is a distinctive dryland ecosystem characterised by a steep natural aridity gradient, transitioning from a coastal hyperarid zone influenced by frequent fog deposition to an inland arid region receiving seasonal rainfall. This study investigates the impact of water availability and moisture regime on microbial trace gas oxidation and community composition across this aridity gradient. Quantitative analyses revealed that total microbial abundance and activity indicators, including ATP concentrations and respiration rates, were significantly (p < 0.005) reduced in hyperarid soils compared to their arid counterparts. In contrast, hyperarid fog-dominated soils exhibited significantly (p < 0.0005) elevated rates of atmospheric hydrogen oxidation, even in the absence of water inputs. We propose that sustained high-affinity hydrogen oxidation, coupled with rapid microbial resuscitation following wetting events, supports shallow sub-surface microbial communities in the Namib Desert, particularly in the coastal hyperarid zone. Together, these findings challenge current understanding of the lower limits of microbial activity and reveal alternate metabolic pathways that enable microbial persistence in hyperarid hot desert soils. ImportanceDrylands are expanding globally, yet the mechanisms that allow microbial life to persist under extreme and sustained water limitation remain poorly understood. This study demonstrates that atmospheric trace gas oxidation, particularly high-affinity hydrogen oxidation, supports active and resilient microbial communities in hyperarid soils of the Namib Desert, even in the absence of liquid water inputs. By revealing how microbes may couple trace gas metabolism to energy and water generation, our findings provide new insight into the lower limits of microbial activity in dry hot desert soils and highlight the need to investigate how microbes persist and sustain soil ecosystem functioning.

microbiology↗

bioRxiv2025

An Asgard archaeon from a modern analog of ancient microbial mats

It has been proposed that eukaryotic cells evolved via symbiosis between sulfate-reducing bacteria and hydrogen-producing archaea. Here we describe a highly enriched culture of a novel Asgard archaeon, Nerearchaeum marumarumayae, with a bacterium Stromatodesulfovibrio nilemahensis from a stromatolite-associated microbial mat. The N. marumarumayae genome indicates it produces H2, acetate, formate, and sulfite, while S. nilemahensis synthesizes amino acids and vitamins, which can be exchanged in a syntrophic partnership. Electron cryotomography revealed N. marumarumayae cells produce chains of budded envelope vesicles attached to the coccoid cell body by extracellular fibers, and intracellular tube- and cage-like structures. Furthermore, the two species were observed interacting via intercellular nanotubes assembled by the bacterium. These characteristics and interactions may reflect an early step in the symbiotic evolution of eukaryotic cells.

microbiology↗

bioRxiv2022

Evidence for a putative isoprene reductase in Acetobacterium wieringae

Recent discoveries of isoprene-metabolizing microorganisms suggest they might play an important role in the global isoprene budget. Under anoxic conditions, isoprene can be used as an electron acceptor and is reduced to methylbutene. This study describes the proteogenomic profiling of an isoprene-reducing bacterial culture to identify organisms and genes responsible for the isoprene hydrogenation reaction. A metagenome assembled genome (MAG) of the most abundant (89% rel. abundance) lineage in the enrichment, Acetobacterium wieringae, was obtained. Comparative proteogenomics and RT-PCR identified a putative five-gene operon from the A. wieringae MAG upregulated during isoprene reduction. The operon encodes a putative oxidoreductase, three pleiotropic nickel chaperones (2 x HypA-like, HypB-like) and one 4Fe-4S ferredoxin. The oxidoreductase is proposed as the putative isoprene reductase with a binding site for NADH, FAD and two pairs of [4Fe-4S]-clusters. Other known Acetobacterium strains do not encode the isoprene-regulated operon but encode, like many other bacteria, a homolog of the putative isoprene reductase ([~]47-49% amino acid sequence identity). Uncharacterized homologs of the putative isoprene reductase are observed across the Firmicutes, Spirochaetes, Tenericutes, Actinobacteria, Chloroflexi, Bacteroidetes and Proteobacteria, suggesting the ability of biohydrogenation of unfunctionalized conjugated doubled bonds in other unsaturated hydrocarbons. ImportanceIsoprene was recently shown to act as an electron acceptor for a homoacetogenic bacterium. The focus of this study is the molecular basis for isoprene reduction. By comparing a genome from our isoprene reducing enrichment culture, dominated by Acetobacterium wieringae, with genomes of other Acetobacterium lineages that do not reduce isoprene, we shortlisted candidate genes for isoprene reduction. Using comparative proteogenomics and reverse transcription PCR we have identified a putative five-gene operon encoding an oxidoreductase referred to as putative isoprene reductase.

microbiology↗

bioRxiv2022

Cross-linking mass spectrometry discovers, evaluates, and validates the experimental and predicted structural proteome

Significant recent advances in structural biology, particularly in the field of cryo-electron microscopy, have dramatically expanded our ability to create structural models of proteins and protein complexes. However, many proteins remain refractory to these approaches because of their low abundance, low stability or - in the case of complexes - simply not having yet been analysed. Here, we demonstrate the power of combining cross-linking mass spectrometry (XL-MS) with artificial intelligence-based structure prediction to discover and experimentally substantiate models for protein and protein complex structures at proteome scale. We present the deepest XL-MS dataset to date, describing 28,910 unique residue pairs captured across 4,084 unique human proteins and 2,110 unique protein-protein interactions. We show that integrative models of complexes driven by AlphaFold Multimer and inspired and corroborated by the XL-MS data offer new opportunities to deeply mine the structural proteome and interactome and reveal new mechanisms underlying protein structure and function.

biochemistry↗

bioRxiv2019

Genomic insights into the Archaea inhabiting an Australian radioactive legacy site

During the 1960s, small quantities of radioactive materials were co-disposed with chemical waste at the Little Forest Legacy Site (LFLS, Sydney, Australia). The microbial function and population dynamics in a waste trench during a rainfall event have been previously investigated using shotgun metagenomics. This revealed a broad abundance of candidate and potentially undescribed taxa in this iron-rich, radionuclide-contaminated environment. Here, applying genome-based metagenomic methods, we recovered 37 refined archaeal MAGs ([≥]50% completeness, [≤]10% redundancy) from 10 different major lineages. They were, mainly, included in four DPANN lineages without standing nomenclature (LFWA-I to IV) and Methanoperedenaceae (ANME-2D). While most of the new DPANN lineages show reduced genomes with limited central metabolism typical of other DPANN, the orders under the LFWA-III lineage, Ca. Gugararchaeales and Ca. Anstonellales, may constitute distinct orders with a more comprehensive central metabolism and anabolic capabilities within the Micrarchaeota phylum. The new Methanoperedens spp. MAGs, together with previously published data, suggests metal ions as the ancestral electron acceptors during the anaerobic oxidation of methane while the respiration of nitrate/nitrite via molybdopterin oxidoreductases would have been a secondary acquisition. The presence of genes for the biosynthesis of polyhydroxyalkanoates in most Methanoperedens also appears to be a widespread characteristic of the genus for carbon accumulation. We formally propose 22 new candidate taxa based on data analysed in this manuscript, as well as four missing formal taxa definitions and two new candidate species based on extant data. We present evidence of four new DPANN lineages and six non-conspecific Methanoperedens, while exploring their uniqueness, potential role in elemental cycling, and evolutionary history.

microbiology↗

bioRxiv2017

Response Of Microbial Community Function To Fluctuating Geochemical Conditions Within A Legacy Radioactive Waste Trench Environment

During the 1960s, small quantities of radioactive materials were co-disposed with chemical waste at the Little Forest Legacy Site (Sydney, Australia) in three-metre-deep, unlined trenches. Chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a six-week period immediately after a prolonged rainfall event to assess how changing water levels impact upon the microbial ecology and contaminant mobility. Collectively, results demonstrated that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solid-iron-associated species immediately after the initial rainwater pulse, to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the potentially important role that the taxonomically-diverse microbial community played in this transition. In particular, aerobes dominated in the first day followed by an increase of facultative anaerobes/denitrifiers at day four. Towards the mid-end of the sampling period, the functional and taxonomic profiles depicted an anaerobic community distinguished by a higher representation of dissimilatory sulfate reduction and methanogenesis pathways. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs.\n\nImportanceThe role of chemical and microbiological factors in mediating the biogeochemistry of groundwaters from trenches used to dispose of radioactive materials during the 1960s is examined in this study. Specifically, chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a six-week period immediately after a prolonged rainfall event to assess how changing water levels influence microbial ecology and contaminant mobility.\n\nResults demonstrate that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solidiron-associated species immediately after the initial rainwater pulse, to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the important role that the taxonomically-diverse microbial community played in this transition. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs.

microbiology↗