Biology subjects

Jones, D. S.

Publications and source records attributed to Jones, D. S..

At least 19 recordsLinked to original sources

bioRxiv2025

Volatilized ammonia supports extremophilic cave ecosystems with unusual nitrogen isotopic signatures

The sulfidic Frasassi cave system hosts a robust, subterranean ecosystem based on microbial lithoautotrophy. Curiously, acidic biofilms forming above degassing sulfidic cave streams, and the invertebrates that feed on them, are extremely depleted in nitrogen-15 ({delta}15N values less than -20{per thousand}). In this study, we tested the hypothesis that these low {delta}15N values result from the volatilization, trapping, and uptake of ammonia degassed from the circumneutral streams. We found that dissolved ammonium in the streams had {delta}15N values near +3{per thousand}, whereas NH3(g) in the cave atmosphere above streams exhibited {delta}15N values as low as -27{per thousand}, consistent with fractionation by NH3 volatilization. Extremely acidic condensation droplets on cave walls efficiently trapped airborne NH3, accumulating up to 4 mM NH4+ with {delta}15N values as low as -29{per thousand}, thereby confirming volatilized and trapped ammonia as the primary N source to cave wall biofilms and the extensive subsurface ecosystem they support. Airborne ammonia trapping represents a novel mechanism for biological N acquisition and provides abundant N for growth in an extreme subsurface environment that otherwise receives very limited nutrient input. SignificanceNitrogen is one of the most abundant elements in organic molecules, and is a key limiting nutrient in many ecosystems. We showed that acidic microbial biofilms in sulfidic caves scavenge trace amounts of airborne ammonia, enabling microbial primary production and supporting associated food webs, including animals, in an environment where nitrogen is otherwise extremely scarce. This process represents a novel mechanism of biological nutrient acquisition and results in biomass and organic matter more depleted in the heavy isotope of nitrogen (15N) than almost all other biological materials on Earth. Extreme 15N isotope depletion is therefore a potential signature of acidic underground ecosystems on Earth and other planetary bodies.

microbiology↗

bioRxiv2025

Gene duplication dynamics and regulatory evolution shape the diversification of Asteraceae

The flowering plant order Asterales exhibits a striking disparity in species richness, with >30,000 species in Asteraceae compared to <50 in its sister family Calyceraceae. To investigate the genomic basis of this imbalance, we assembled three new chromosome-level genomes, including the first for Calyceraceae, and re-annotated five additional genomes. Comparative analyses revealed exceptionally high repeat content in both Asteraceae and Calyceraceae, pervasive chromosomal rearrangements, and evidence for shared and lineage-specific WGDs. In Asteraceae, tandem and dispersed duplications disproportionately drove expansions of gene families linked to secondary metabolism and stress response, while segmental duplicates bore signatures of adaptive selection for the regulation of biosynthetic and metabolic processes. Selective pressures on flowering time regulators suggest an evolved balance between regulatory flexibility and developmental constraint in floral diversification. These patterns reveal that, beyond ancient polyploidy, small-scale duplications and selective fine-tuning of regulatory networks underpinned the ecological versatility in Asteraceae, fueling its extraordinary diversification.

genomics↗

bioRxiv2025

Diverse but temporally stable virome in a 1.2 km deep karst aquifer accessed via Moab Khotsong mine, South Africa

Despite their ubiquity, viruses remain understudied in many of Earths environments. The deep subsurface contains a large portion of Earths biomass and can be expected to hold a rich store of viruses as well. We investigated the viral community in a 1.2-kilometer-deep dolomitic aquifer accessed in the Moab Khotsong gold mine in South Africa by microscopically quantifying virus-like particles (VLP) and cells and conducting a metagenomic survey of viruses and their associations with the microbial community. VLP:cell ratios were consistently lower ([~]1:1) than those found in most shallower aquifers. Viral sequences were recovered from both the <0.2 {micro}m fraction, presumably representing free virions, and the >0.2 {micro}m fraction that also included microbial cells. Viruses were diverse and 78% were novel, and the viral communities were relatively unchanged at four sampling dates spanning five years. Host prediction indicated viral infection of the dominant microbes, including Thiomicrospiraceae and Rhodocyclaceae, with temperate phages. Viral genomes include auxiliary metabolic genes (AMGs), with most of them being Type II, which favor host persistence. Taken together, VLP:cell ratios, type II AMGs, and temporally stable viromes point to dominance of lysogeny and piggyback-the-persistent viral-host interactions in the deep aquifer. The many novel viruses observed here suggest that the terrestrial subsurface is an untapped reservoir of viral diversity.

microbiology↗

bioRxiv2025

Floral innovation through modifications in stem cell peptide signaling.

Understanding how evolution shapes genetic networks to create new developmental forms is a central question in biology. Asteraceae (sunflower family) comprise 10% of flowering plants and have capitula, a novel flowering shoot (inflorescence) that mimics a single flower (1, 2). During capitulum development, shoot stem cells undergo prolonged proliferation relative to other species (3, 4). Here we show that capitulum evolution paralleled decreases in CLAVATA3 peptide (CLV3p) signaling, a conserved repressor of stem cell proliferation. Asteraceae CLV3p displays reduced receptor binding and downstream transcriptional outputs. Reversion of CLV3 to a more active form impairs Asteraceae stem cell regulation and capitulum development. Lastly, we trace CLV3 evolution across the Asterales allowing inferences on capitulum evolution. Our findings reveal novel evolutionary mechanisms in plant reproduction and suggest approaches for engineering crops.

plant biology↗

bioRxiv2025

Canalization of flower production across thermal environments requires Florigen and CLAVATA signaling.

The ability to maintain invariant developmental phenotypes across disparate environments is termed canalization, but few examples of canalization mechanisms are described. In plants, robust flower production across environmental gradients contributes to reproductive success and agricultural yields. Flowers are produced by the shoot apical meristem (SAM) in an auxin-dependent manner following the switch from vegetative growth to the reproductive phase. While the timing of this phase change, called the floral transition, is sensitized to numerous environmental and endogenous signals, flower formation itself is remarkably invariant across environmental conditions. Previously we found that CLAVATA peptide signaling promotes auxin-dependent flower primordia formation in cool environments, but that high temperatures can restore primordia formation through unknown mechanisms. Here, we show that heat promotes floral primordia patterning and formation in SAMs not by increased auxin production, but through the production of the mobile flowering signal, florigen, in leaves. Florigen, which includes FLOWERING LOCUS T (FT) and its paralog TWIN SISTER OF FT (TSF) in Arabidopsis thaliana, is necessary and sufficient to buffer flower production against the loss of CLAVATA signaling and promotes heat-mediated primordia formation through specific SAM expressed transcriptional regulators. We find that sustained florigen production is necessary for continuous flower primordia production at warmer temperatures, contrasting florigens switch-like control of floral transition. Lastly, we show that CLAVATA signaling and florigen synergize to canalize flower production across broad temperature ranges. This work sheds light on the mechanisms governing the canalization of plant development and provides potential targets for engineering crop plants with improved thermal tolerances.

plant biology↗

bioRxiv2025

Historic mine waste contains diverse microbial communities that reflect waste type and geochemistry

Waste rock and tailings left behind by historic mining operations can contain substantial critical mineral resources. However, over the decades and centuries since these deposits were emplaced, microbial communities developed that can catalyze rock weathering and elemental cycling, which could have impacted the economic resources but also might be harnessed for future biomining or other metal recovery efforts. Here we combined cell counting, rRNA gene and transcript sequencing, and whole rock geochemistry to compare the composition and abundance of microbial communities from five inactive mine sites in South-Central New Mexico that contain critical minerals. While acidic seeps and adits at the sites contained organisms commonly found in acid rock drainage and bioleaching operations, these organisms were only present at very low abundance in the waste rock and tailings, which were instead dominated by bacteria and archaea that mostly represent inorganic nitrogen- and organic carbon-oxidizing populations. Generally, rRNA transcript libraries contained many of the same organisms as rRNA gene libraries, indicating that most of these microbial populations are active. Differences among total and active communities correspond to waste rock geochemistry, including concentrations of sulfur, iron, and other variables such as copper, lead, and rare earth elements. Nevertheless, many of the rRNA gene and transcript sequences in these deposits were from groups without cultured representatives, and these unknown microorganisms are likely important for biogeochemical cycling over the long lifetime of these waste deposits. We also discuss recommendations for microbiological assessment of similar large historic mine waste deposits. IMPORTANCENew Mexico has a long history of mining, with hundreds of mining districts across the state, many of which contain inactive operations with historic tailings and waste rock. Because metallurgical processing was in its infancy when most of these mines were active, they contain substantial metal resources in tailings and waste rock that could be used to support domestic demand for critical minerals. We found that microbial communities associated with these deposits do not represent typical bioleaching communities, and instead are dominated by taxa not typically associated with mine wastes. However, the deposits do contain rare iron and sulfur-cycling taxa that could catalyze metal mobilization, as well as active populations of novel microorganisms that are likely important for biogeochemical cycling. These mine waste-associated microbial communities could represent important resources for bioremediation and other biotechnological applications to recover valuable elements from these and other historic mine waste deposits.

microbiology↗

bioRxiv2025

A Syntenic Pangenome for Gardnerella Reveals Taxonomic Boundaries and Stratification of Metabolic and Virulence Potential across Species

Gardnerella species are central to bacterial vaginosis (BV), a condition affecting nearly one in three women of reproductive age and associated with preterm birth and increased susceptibility to sexually transmitted infections. Despite decades of study, progress in defining Gardnerella diversity has been hindered by inconsistent taxonomy and poor-quality genomic resources. Here, we sequenced 392 new Gardnerella isolates from asymptomatic and BV-associated microbiota and integrated this collection with all publicly available genomes. After stringent curation, we generated a high-quality reference set of 313 distinct genomes that underpins a comprehensive taxonomic framework. Using average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and phylogenomics, we resolved 21 genomic lineages encompassing 11 species and 15 subspecies, each assigned a provisional formal name. Integration of complete long-read assemblies enabled construction of the first syntenic Gardnerella pangenome, revealing lineage-specific repertoires of virulence, metabolic, and defense systems - including variable sialidases (NanH), vaginolysin, and amino-acid biosynthetic pathways - and defining conserved genomic architecture across species. Comparative methylome profiling further highlighted restriction-modification system diversity that may influence genetic exchange. Finally, we identified the first native cryptic plasmids in Gardnerella, overturning the assumption that the genus lacks plasmids, and demonstrated their use in generating a replicative E. coli-Gardnerella shuttle vector. Together, these results establish a complete genomic and functional framework for Gardnerella, providing a reproducible foundation for mechanistic and translational studies of BV and a model for resolving taxonomy and functional stratification in other urogenital-associated bacteria.

microbiology↗

bioRxiv2025

Microbial ecology of acidic, biogenic gypsum: Community structure and distribution of extremophiles on freshly formed and relict sulfate deposits in a hydrogen sulfide-rich cave

Sulfate minerals are abundant on the Martian surface, and many of these evaporite deposits are thought to have precipitated from acidic fluids. On Earth, gypsum (CaSO4*2H2O) and other sulfates sometimes form under acidic conditions, so exploring the extremophilic life that occurs in these mineral environments can help us evaluate the astrobiological potential of acid sulfate depositional settings. Here, we characterized the microbial communities associated with acidic gypsum deposits in a sulfuric acid cave, where sulfate precipitation is driven by sulfide-oxidizing bacteria and archaea. We used 16S rRNA gene sequencing and cell counts to characterize gypsum-associated microorganisms in freshly formed and relict deposits throughout the cave, in order to test hypotheses about how microbial community composition and abundance would vary with distance from the sulfidic water table and with the concentration of H2S(g) and other gases in the cave atmosphere. We found that actively-forming gypsum in the lower cave levels was colonized by low diversity communities of sulfide-oxidizing chemolithotrophs and other acidophiles that have few cells compared to other environments in the cave. The most abundant taxa were Acidithiobacillus, Metallibacterium, Mycobacteria, and three different Thermoplasmatales-group archaea, which occupied distinct niches based on proximity to sulfidic streams and the concentration of gases in the cave air. In contrast, deposits in older cave levels had more diverse communities that are dominated by chemoorganotrophic and methanotrophic taxa. These findings show that acidic sulfate deposits serve as habitats for extremophilic microorganisms, and broaden our knowledge of the life associated with terrestrial sulfates. ImportanceGypsum and other sulfate salts are common on Mars, and many of these deposits are thought to have formed from acidic fluids early in the planets history. Understanding the life that survives and thrives in similar environments on Earth is therefore crucial for evaluating whether these Martian sulfates are or ever were habitable. One such environment where acidic gypsum occurs is in sulfuric acid caves, where extremophilic microorganisms drive the precipitation of sulfate minerals by oxidizing hydrogen sulfide gas from the cave atmosphere. Here, we characterized the communities of microorganisms on freshly formed and ancient gypsum in the Frasassi Caves, and found that the gypsum deposits hosted microbial communities that changed based on chemical energy availability and the age of the gypsum. Our findings underscore the importance of chemical and microbiological interactions in shaping habitable niches, and provide context for searching for past or present life in acidic Martian sulfates.

microbiology↗

bioRxiv2025

Sulfuriferula spp. from sulfide mineral weathering environments have diverse sulfur- and iron-cycling capabilities

Microorganisms are important catalysts for the oxidation of reduced inorganic sulfur compounds. One environmentally important source of reduced sulfur is metal sulfide minerals that occur in economic mineral deposits and mine waste. Previous research found that Sulfuriferula spp. were abundant and active in long-term weathering experiments with simulated waste rock and tailings from the Duluth Complex, Northern Minnesota. We therefore isolated several strains of Sulfuriferula spp. from these long-term experiments and characterized their metabolic and genomic properties to provide insight into microbe-mineral interactions and the microbial biogeochemistry in these and other moderately acidic to circumneutral environments. The Sulfuriferula strains are all obligate chemolithoautotrophs capable of oxidizing inorganic sulfur compounds and ferrous iron. The strains grew over different pH ranges, but all grew between pH 4.5-7, matching the weathering conditions of the Duluth Complex rocks. All strains grew on the iron-sulfide mineral pyrrhotite (Fe1-xS, 0 < x < 0.125) as the sole energy source, as well as hydrogen sulfide and thiosulfate, which are products of sulfide mineral breakdown. Despite their metabolic similarities, each strain encodes a distinct pathway for the oxidation of reduced inorganic sulfur compounds as well as differences in nitrogen metabolism that reveal diverse genomic capabilities among the group. Our results show that Sulfuriferula spp. are primary producers that likely play a role in sulfide mineral breakdown in moderately acidic to circumneutral mine waste, and the metabolic diversity within the genus likely explains their success in sulfide mineral-rich and other sulfidic environments. ImportanceMetal sulfide minerals such as pyrite and pyrrhotite are one of the main sources of reduced sulfur in the global sulfur cycle. The chemolithotrophic microorganisms that break down these minerals in natural and engineered settings are catalysts for biogeochemical sulfur cycling and have important applications in biotechnological processes such as biomining or bioremediation. Sulfuriferula is a recently described genus of sulfur oxidizing bacteria that are abundant primary producers in diverse terrestrial environments, including waste rock and tailings from metal mining operations. In this study, we explored the genomic and metabolic properties of new isolates from this genus, and the implications for their ecophysiology and biotechnological potential in ore and waste from economic mineral deposits.

microbiology↗

bioRxiv2024

Cave pools in Carlsbad Caverns National Park contain diverse bacteriophage communities and novel viral sequences

Viruses are the most abundant biological entities on Earth, and they play a critical role in the environment and biosphere where they regulate microbial populations and contribute to nutrient cycling. Environmental viruses have been the most studied in the ocean, but viral investigations have now spread to other environments. Here, viral communities were characterized in four cave pools in Carlsbad Caverns National Park to test the hypotheses that (i) viral abundance is ten-fold higher than prokaryotic cell abundance in cavern pools, (ii) cavern pools contain novel viral sequences, and (iii) viral communities in pools from developed portions of the cave are distinct from those of pools in undeveloped parts of the same cave. The relationship between viral and microbial abundance was determined through direct epifluorescence microscopy counts. Viral metagenomes were constructed to examine viral diversity among pools, identify novel viruses, and characterize auxiliary metabolic genes (AMGs). Bacterial communities were characterized by 16S rRNA gene amplicon sequencing. Epifluorescence microscopy showed that the ratio of viral-like particles (VLPs) to microorganisms was approximately 22:1 across all sites. Viral communities from pools with higher tourist traffic were more similar to each other than to those from less visited pools, although surprisingly, viruses did not follow the same pattern as bacterial communities, which reflected pool geochemistry. Bacterial hosts predicted from viral sequences using iPHoP showed overlap with both rare and abundant genera and families in the 16S rRNA gene dataset. Gene-sharing network analysis revealed high viral diversity compared to a reference viral database as well as to other aquatic environments. AMG presence showed variation in metabolic potential among the four pools. Overall, Carlsbad Cavern harbors novel viruses with substantial diversity among pools within the same system, indicating that caves are likely an important repository for unexplored viromes.

microbiology↗

bioRxiv2024

Metagenomic insights into an enigmatic gammaproteobacterium that is important for carbon cycling in cave ecosystems worldwide

Caves are windows into the subsurface through which we can directly evaluate the microbiological processes responsible for rock weathering and biogeochemical cycling in more expansive areas of Earths subsurface. However, many cave microbial communities are dominated by microorganisms from uncultivated groups with unknown genomic capabilities that cannot be resolved from marker gene surveys alone. An example of this is a genus of Gammaproteobacteria known as "wb1-P19", which are ubiquitous and abundant in rRNA gene surveys from limestone and volcanic caves around the world. We recovered a nearly complete metagenome-assembled genome (MAG) representing a population of wb1-P19 from Lehman Caves in Great Basin National Park, Nevada, USA, and used it to identify additional MAGs representing this group from the Frasassi Caves in Italy and in publicly available databases. Although members of the wb1-P19 group have often been thought to be autotrophs that oxidize inorganic nitrogen compounds, we show that wb1-P19 are actually obligate or facultative methanotrophs capable of aerobic and anaerobic growth. Based on genomic classification, wb1-P19 are members of upland soil cluster {gamma} (USC{gamma}; part of the newly proposed order "Candidatus Methyloligotrophales"), and are likely important for methane consumption and carbon cycling in caves and other subterranean ecosystems globally.

microbiology↗

bioRxiv2023

Origin and modern microbial ecology of secondary mineral deposits in Lehman Caves, Great Basin National Park, NV, USA

Lehman Caves is an extensively decorated, high desert cave that represents one of the main tourist attractions in Great Basin National Park, Nevada. Although traditionally considered a water table cave, recent studies identified abundant speleogenetic features consistent with a hypogenic and, potentially, sulfuric acid origin. Here, we characterized white mineral deposits in the Gypsum Annex (GA) passage to determine whether these secondary deposits represent biogenic minerals formed during sulfuric acid corrosion, and explored microbial communities associated with these and other mineral deposits throughout the cave. Powder X-ray diffraction (pXRD), scanning electron microscopy with electron dispersive spectroscopy (SEM-EDS), and electron microprobe analyses (EPMA) showed that, while most white mineral deposits from the GA contain gypsum, they also contain abundant calcite, silica, and other phases. Gypsum and carbonate-associated sulfate isotopic values of these deposits are variable, with {delta}34SV-CDT between +9.7{per thousand} and +26.1{per thousand}, and do not reflect depleted values typically associated with replacement gypsum formed during sulfuric acid speleogenesis. Petrographic observations show that the sulfates likely co-precipitated with carbonate and SiO2 phases. Taken together, these data suggest that the deposits resulted from later stage meteoric events and not during an initial episode of sulfuric acid speleogenesis. Most sedimentary and mineral deposits in Lehman Caves have very low microbial biomass, with the exception of select areas along the main tour route that have been impacted by tourist traffic. High-throughput 16S rRNA gene amplicon sequencing showed that microbial communities in GA sediments are distinct from those in other parts of the cave. The microbial communities that inhabit these oligotrophic secondary mineral deposits include OTUs related to known ammonia-oxidizing Nitrosococcales and Thaumarchaeota, as well as common soil taxa such as Acidobacteriota and Proteobacteria. This study reveals microbial and mineralogical diversity in a previously understudied cave and expands our understanding of the geomicrobiology of arid, hypogene cave systems.

microbiology↗

bioRxiv2023

Compositae-ParaLoss-1272: Complementary sunflower specific probe-set reduces issues with paralogs in complex systems

PremiseThe sunflower family specific probe set, Compositae-1061, has enabled family-wide phylogenomic studies and investigations at lower-taxonomic levels by targeting 1,000+ genes. However, it generally lacks resolution at the genus to species level, especially in groups with complex evolutionary histories including polyploidy and hybridization. MethodsIn this study, we developed a new Hyb-Seq probe set, Compositae-ParaLoss-1272, designed to target orthologous loci in Asteraceae family members. We tested its efficiency across the family by simulating target-enrichment sequencing in silico. Additionally, we tested its effectiveness at lower taxonomic levels in genus Packera which has a complex evolutionary and taxonomic history. We performed Hyb-Seq with Compositae-ParaLoss-1272 for 19 taxa which were previously studied using the Compositae-1061 probe set. Sequences from both probe sets were used to generate phylogenies, compare topologies, and assess node support. ResultsWe report that Compositae-ParaLoss-1272 captured loci across all tested Asteraceae members. Additionally, Compositae-ParaLoss-1272 had less gene tree discordance, recovered considerably fewer paralogous sequences, and retained longer loci than Compositae-1061. DiscussionGiven the complexity of plant evolutionary histories, assigning orthology for phylogenomic analyses will continue to be challenging. However, we anticipate this new probe set will provide improved resolution and utility for studies at lower-taxonomic levels and complex groups in the sunflower family.

plant biology↗

bioRxiv2023

Fusobacterium sphaericum sp. nov., isolated from a human colon tumor, is prevalent in various human body sites and induces IL-8 secretion from colorectal cancer cells

Cancerous tissue is a largely unexplored microbial niche that provides a unique environment for the colonization and growth of specific bacterial communities, and with it, the opportunity to identify novel bacterial species. Here, we report distinct features of a novel Fusobacterium species, F. sphaericum sp. nov. (Fs), isolated from primary colon adenocarcinoma tissue. We acquire the complete closed genome and associated methylome of this organism and phylogenetically confirm its classification into the Fusobacterium genus, with F. perfoetens as its closest neighbor. Fs is phenotypically and genetically distinct, with morphological analysis revealing its coccoid shape, that while similar to F. perfoetens is rare for most Fusobacterium members. Fs displays a metabolic profile and antibiotic resistance repertoire consistent with other Fusobacterium species. In vitro, Fs has adherent and immunomodulatory capabilities, as it intimately associates with human colon cancer epithelial cells and promotes IL-8 secretion. Analysis of the prevalence and abundance of Fs in >20,000 human metagenomic samples shows that it is a low-prevalence member within human stool with variable relative abundance, found in both healthy controls and patients with colorectal cancer (CRC). Our study sheds light on a novel bacterial species isolated directly from the human CRC tumor niche, and given its interaction with cancer epithelial cells suggests that its role in human health and disease warrants further investigation.

microbiology↗

bioRxiv2022

Microbial communities from weathered outcrops of a sulfide-rich ultramafic intrusion, and implications for mine waste management

The Duluth Complex, Northeastern Minnesota, contains sulfide-rich magmatic intrusions that, collectively, represent one of the worlds largest known economic deposits of copper, nickel, and platinum group elements (Cu-Ni-PGEs). Previous work showed that microbial communities associated with experimentally-weathered Duluth Complex waste rock and tailings were dominated by uncultivated taxa and other populations not typically associated with mine waste. However, those experiments were designed for kinetic testing and do not necessarily represent the conditions expected for reclaimed mine waste or long-term weathering in the environment. We therefore used 16S rRNA gene methods to characterize the microbial communities present on the surfaces of naturally-weathered and historically disturbed outcrops of Duluth Complex material, as well as a circumneutral seep draining a reclaimed blast pit. Rock surfaces were dominated by diverse uncultured Ktedonobacteria, Acetobacteria, and Actinobacteria while seeps were dominated by Proteobacteria, including Leptothrix spp. and Methylovulum spp. All samples had abundant algae and other phototrophs. These communities were distinct from previously-described microbial assemblages from experimentally-weathered Duluth Complex rocks, suggested different energy and nutrient resources in the reclaimed rocks, outcrops, and seeps. Sulfide mineral incubations performed with and without algae showed that photosynthetic microorganisms could have an inhibitory effect on some of the autotrophic populations from the site, resulting in slightly lower sulfate release and differences in the dominant microorganisms. The microbial assemblages from these weathered outcrops show how communities are expected to develop during natural weathering of sulfide-rich Duluth Complex rocks, and represent baseline data that could be used to evaluate the effectiveness of future reclamation of tailings and waste rock produced by large scale mining operations.

microbiology↗

bioRxiv2022

Convergent community assembly among globally separated acidic cave biofilms

Acidophilic bacteria and archaea inhabit extreme geochemical islands that can tell us when and how geographic barriers affect the biogeography of microorganisms. Here we describe microbial communities from extremely acidic (pH 0-1) biofilms known as "snottites" from hydrogen sulfide-rich caves around the world. Given the extreme acidity and subsurface location of these biofilms, and in light of earlier work showing strong geographic patterns among snottite Acidithiobacillus populations, we investigated their structure and diversity in order to understand how geography might impact community assembly. We used 16S rRNA gene cloning and fluorescence in situ hybridization (FISH) to investigate 26 snottite samples from four sulfidic caves in Italy and Mexico. All samples had very low biodiversity and were dominated by sulfur-oxidizing bacteria in the genus Acidithiobacillus. Ferroplasma and other archaea in the Thermoplasmatales ranged from 0 to 50% of total cells, and relatives of the bacterial genera Acidimicrobium and Ferrimicrobium were up to 15% of total cells. Rare phylotypes included Sulfobacillus spp. and members of the Dependentiae and Saccharibacteria (formerly TM6 and TM7). Although the same genera of acidophiles occurred in snottites on separate continents, most members of those genera represent substantially divergent populations with 16S rRNA genes that are only 95-98% similar. Our findings are consistent with a model of community assembly where sulfidic caves are stochastically colonized by microorganisms from local sources, which are strongly filtered through selection for extreme acid tolerance, and these different colonization histories are maintained by dispersal restrictions within and among caves. ImportanceMicroorganisms that are adapted to extremely acidic conditions, known as extreme acidophiles, are catalysts for rock weathering, metal cycling, and mineral formation in naturally acidic environments. They are also important drivers of large-scale industrial processes such as biomining and contaminant remediation. Understanding the factors that govern their ecology and distribution can help us better predict and utilize their activities in natural and engineered systems. However, extremely acidic habitats are unusual in that they are almost always isolated within circumneutral landscapes. So where did their acid-adapted inhabitants come from, and how do new colonists arrive and become established? In this study, we took advantage of a unique natural experiment in Earths subsurface to show how isolation may have played a role in the colonization history, community assembly, and diversity of highly acidic microbial biofilms.

microbiology↗

bioRxiv2022

Helicobacter pylori chronic infection selects for effective colonizers of metaplastic glands

Chronic gastric infection with Helicobacter pylori can lead to progressive tissue changes that culminate in cancer, but how H. pylori adapts to the changing tissue environment during disease development is not fully understood. In a transgenic mouse gastric metaplasia model, we found that strains from unrelated individuals differed in their ability to infect the stomach, to colonize metaplastic glands, and to induce proliferation and alter the expression of metaplasia-associated proteins. H. pylori isolates from different stages of disease from a single individual had differential ability to colonize healthy and metaplastic gastric glands. Exposure to the metaplastic environment selected for high gastric colonization by one of these strains. Complete genome sequencing revealed a unique alteration in the frequency of a variant allele of the putative adhesin sabB, arising from a recombination event with the related sialic acid binding adhesin (SabA) gene. Mutation of sabB strongly reduced adherence to both normal and metaplastic gastric tissue in multiple strain backgrounds and highly attenuated stomach colonization. Thus, the changing gastric environment during disease development promotes bacterial adhesin gene variation associated with enhanced gastric colonization. ImportanceChronic infection with Helicobacter pylori is the primary risk factor for developing stomach cancer. As disease progresses H. pylori must adapt to a changing host tissue environment that includes induction of new cell fates in the cells that line the stomach. We tested representative H. pylori isolates collected from the same patient during early and later stages of disease in a mouse model where we can rapidly induce disease-associated tissue changes. Only the later-stage H. pylori strains could robustly colonize the diseased stomach environment. We also found that the ability to colonize the diseased stomach was associated with genetic variation in a putative cell surface adhesin gene called sabB. Additional experiments revealed that SabB promotes binding to stomach tissue and is critical for stomach colonization by the late-stage strains. Thus, H. pylori diversifies its genome during disease progression and these genomic changes highlight critical factors for bacterial persistence.

microbiology↗

bioRxiv2022

A network of CLAVATA receptors buffers auxin-dependent meristem maintenance

Plant body plans are elaborated in response to both environmental and endogenous cues. How these inputs intersect to promote growth and development remains poorly understood. During reproductive development, central zone stem cell proliferation in inflorescence meristems is negatively regulated by the CLAVATA3 (CLV3) peptide signaling pathway. In contrast, floral primordia formation on meristem flanks requires the hormone auxin. Here we show that CLV3 signaling is also necessary for auxin-dependent floral primordia generation and that this function is partially masked by both inflorescence fasciation and heat-induced auxin biosynthesis. Stem cell regulation by CLAVATA signaling is separable from primordia formation but is also sensitized to temperature and auxin levels. Additionally, we uncover a novel role for the CLV3 receptor CLAVATA1 in auxin- dependent meristem maintenance in cooler environments. As such, CLV3 signaling buffers multiple auxin-dependent shoot processes across divergent thermal environments with opposing effects on cell proliferation in different meristem regions.

plant biology↗