Ultra-small bacteria and archaea exhibit genetic flexibility towards groundwater oxygen content, and adaptations for attached or planktonic lifestyles

Particle size transfer of antibiotic resistance genes in typical processes of municipal wastewater treatment plant

Occurrence and transfer of antibiotic resistance genes (ARGs) was investigated concerning sludge particle size in a typical wastewater treatment plant, and the roles of vertical (VGT) and horizontal gene transfer (HGT) in the spread of ARGs were explored. Results showed that although membrane bioreactor (MBR) effectively reduced the relative abundance of ARGs in the water phase, it concurrently enriched ARGs in MBR sludge, particularly for the largest-size particles (>150 μm). A decreasing trend in the relative abundance of ARGs was observed along with the decrease of sludge particle size, and larger-size particle sludge (>106 μm) formed a relatively stable composition of ARGs, while ARGs on smaller-size particle sludge (6.5-106 μm) fluctuate rapidly. Particle size does not affect the abundance distribution patterns or assembly mechanisms of ARGs as deterministic processes. The smallest-size particles were the primary attachment site for bacterial pathogens with highest diversity. Larger-size particle sludge (>106 μm) showed higher frequency of HGT, with Proteobacteria as the dominant hosts for this process.

Biogeography and ecological functions of underestimated CPR and DPANN in acid mine drainage sediments

Recent genomic surveys have uncovered candidate phyla radiation (CPR) bacteria and DPANN archaea as major microbial dark matter lineages in various anoxic habitats. Despite their extraordinary diversity, the biogeographic patterns and ecological implications of these ultra-small and putatively symbiotic microorganisms have remained elusive. Here, we performed metagenomic sequencing on 90 geochemically diverse acid mine drainage sediments sampled across southeast China and recovered 282 CPR and 189 DPANN nonredundant metagenome-assembled genomes, which collectively account for up to 28.6% and 31.2% of the indigenous prokaryotic communities, respectively. We found that, remarkably, geographic distance represents the primary factor driving the large-scale ecological distribution of both CPR and DPANN organisms, followed by pH and Fe. Although both groups might be capable of iron reduction through a flavin-based extracellular electron transfer mechanism, significant differences are found in their metabolic capabilities (with complex carbon degradation and chitin degradation being more prevalent in CPR whereas fermentation and acetate production being enriched in DPANN), indicating potential niche differentiation. Predicted hosts are mainly Acidobacteriota, Bacteroidota, and Proteobacteria for CPR and Thermoplasmatota for DPANN, and extensive, unbalanced metabolic exchanges between these symbionts and putative hosts are displayed. Together, our results provide initial insights into the complex interplays between the two lineages and their physicochemical environments and host populations at a large geographic scale.IMPORTANCECandidate phyla radiation (CPR) bacteria and DPANN archaea constitute a significant fraction of Earth's prokaryotic diversity. Despite their ubiquity and abundance, especially in anoxic habitats, we know little about the community patterns and ecological drivers of these ultra-small, putatively episymbiotic microorganisms across geographic ranges. This study is facilitated by a large collection of CPR and DPANN metagenome-assembled genomes recovered from the metagenomes of 90 sediments sampled from geochemically diverse acid mine drainage (AMD) environments across southeast China. Our comprehensive analyses have allowed first insights into the biogeographic patterns and functional differentiation of these major enigmatic prokaryotic groups in the AMD model system.

Nannochloropsis oceanica IMET1 and its bacterial symbionts for carbon capture, utilization, and storage: biomass and calcium carbonate production under high pH and high alkalinity

To combat the increasing levels of carbon dioxide (CO2) released from the combustion of fossil fuels, microalgae have emerged as a promising strategy for biological carbon capture, utilization, and storage. This study used a marine microalgal strain, Nannochloropsis oceanica IMET1, which thrives in high CO2 concentrations. A high-pH, high-alkalinity culture was designed for CO2 capture through algal biomass production as well as permanent sequestration through calcium carbonate (CaCO3) precipitation. This was accomplished by timed pH elevation and the addition of sodium bicarbonate to cultures of N. oceanica grown at lab scale (1 L) and pilot scale (500 L) with 10% and 5% CO2, respectively. Our data showed that 0.02 M NaHCO3 promoted algal growth and that sparging cultures with ambient air after 12 days raised pH and created favorable CaCO3 formation conditions. At the 1 L scale, we reached 1.52 g L-1 biomass after 12 days and an extra 9.3% CO2 was captured in the form of CaCO3 precipitates. At the 500 L pilot scale, an extra 60% CO2 was captured (Day 40) with a maximum CO2 capture rate of 63.2 g m-2 day-1 (Day 35). Bacterial communities associated with the microalgae were dominated by two novel Patescibacteria. Functional analysis revealed that genes for several plant growth-promotion traits (PGPTs) were enriched within this group. The microalgal-bacterial coculture system offers advantages for enhanced carbon mitigation through biomass production and simultaneous precipitation of recalcitrant CaCO3 for long-term CO2 storage.IMPORTANCECapturing carbon dioxide (CO2) released from fossil fuel combustion is of the utmost importance as the impacts of climate change continue to worsen. Microalgae can remove CO2 through their natural photosynthetic pathways and are additionally able to convert CO2 into a stable, recalcitrant form as calcium carbonate (CaCO3). We demonstrate that microalgae-based carbon capture systems can be greatly improved with high pH and high alkalinity by providing optimal conditions for carbonate precipitation. Our results with the microalga, Nannochloropsis oceanica strain IMET1, show an extra 9.3% CO2 captured as CaCO3 at the 1 L scale and an extra 60% CO2 captured at the 500 L (pilot) scale. Our optimized system provides a novel approach to capture CO2 through two mechanisms: (i) as organic carbon within microalgal biomass and (ii) as inorganic carbon stored permanently in the form of CaCO3.

Site-specific incubations reveal biofilm diversity and functional adaptations in deep, ancient desert aquifers

Deep pristine aquifers are ecological hotspots with diverse microbial life, where microorganisms exist either attached (sessile) to solid substrates or suspended in groundwater (planktonic). Characterizing the attached microbial communities is of paramount importance, especially in the context of biofouling. However, obtaining samples of attached microbes that thrive under natural (undisturbed) conditions is challenging. Our study addresses this by retrieving sessile microbes on-site. We installed columns filled with site-specific rock cuttings at the wellhead, allowing fresh groundwater to flow continuously for approximately 60 days. We hypothesized that the attached microbial communities would differ structurally from planktonic microbes due to the aquifer's lithological and mineralogical composition. This study involved an exploratory examination of the microbial communities in different aquifers with distinct mineralogies, including quartzitic sandstone, calcareous, chert, and highly heterogeneous (clastic) aquifers in Israel's Negev Desert. Metagenomic analysis revealed both shared and distinct microbial communities among attached and planktonic forms in the various environments, likely shaped by the aquifers' physical, lithological, and mineralogical properties. A wealth of carbon-fixation pathways and energy-conservation strategies in the attached microbiome provide evidence for the potential productivity of these biofilms. We identified widespread genetic potential for biofilm formation (e.g., via pili, flagella, and extracellular polymeric substance production) and the interactome (e.g., quorum-sensing genes). Our assessment of these functions provides a genomic framework for groundwater management and biofouling treatment.

Protozoa-enhanced conjugation frequency alters the dissemination of soil antibiotic resistance

Protozoa, as primary predators of soil bacteria, represent an overlooked natural driver in the dissemination of antibiotic resistance genes (ARGs). However, the effects of protozoan predation on ARGs dissemination at the community level, along with the underlying mechanisms, remain unclear. Here we used fluorescence-activated cell sorting, qPCR, combined with metagenomics and reverse transcription quantitative PCR, to unveil how protozoa (Colpoda steinii and Acanthamoeba castellanii) influence the plasmid-mediated transfer of ARGs to soil microbial communities. Protozoan predation reduced the absolute abundance of plasmids but promoted the expression of conjugation-associated genes, leading to a 5-fold and 4.5-fold increase in conjugation frequency in the presence of C. steinii and A. castellanii, respectively. Excessive oxidative stress, increased membrane permeability, and the provoked SOS response closely associated with the increased conjugative transfer. Protozoan predation also altered the plasmid host range and selected for specific transconjugant taxa along with ARGs and virulence factors carried by transconjugant communities. This study underscores the role of protozoa in the plasmid-mediated conjugative transfer of ARGs, providing new insights into microbial mechanisms that drive the dissemination of environmental antibiotic resistance.

Eutrophication impacts the distribution and functional traits of viral communities in lakes

Viruses play a crucial role in aquatic ecosystems by regulating microbial composition and impacting biogeochemical cycling. While the response of viral diversity to the trophic status has been preliminarily explored in lake ecosystems, there is limited integrated exploration of the biogeography of viruses, host associations, and the auxiliary metabolic genes (AMGs), particularly for plateau lakes. Therefore, this research investigated the viral biogeography, virus-host association, and AMGs in the surface waters of 11 lakes varying in trophic levels (eutrophic and oligo-mesotrophic) in the Yunnan-Guizhou plateau region of China. A total of 73,105 viral operational taxonomic units were obtained from 11 samples, with 84.8 % remaining unannotated at the family level, indicating a predominance of novel viruses within these lakes. The most abundant viral family was Kyanoviridae (24.4 %), recognized as a common cyanophage. The vast majority of cyanobacteria and several eukaryotic algae were predicted as hosts for the viruses, with a lytic lifestyle predominating the life strategy of these cyanophages, implying the potential influence of the virus on algae. The viral community structure significantly correlated with both trophic status and the bacterial community. The structure equation model analysis revealed chlorophyll a was the primary factor affecting viral communities. Moreover, numerous AMGs linked to carbon metabolism, phosphorus metabolism, sulfur metabolism, and photosynthesis were found in these lakes, some of which showed virus preference for the trophic statuses, suggesting a vital role of the virus in driving biogeochemical cycling in the lake crossing different nutrient levels. In addition, a restricted presence of viruses was found to infect humans or harbor antibiotic resistance genes in the lakes, suggesting a subtle yet potential link to human health. Overall, these findings offer insights into the response of viral communities to eutrophication and their potential role in biogeochemical cycling and controlling algal propagation.

Viral Diversity and Ecological Impact of DNA Viruses in Dominant Tick Species in China

Ticks are blood-feeding ectoparasites that also transmit various pathogens, posing severe risks to human and animal health. DNA viruses play a crucial role in the microbial ecology of ticks, but their distribution and ecological significance remain largely undetermined. Here, we assembled an extensive catalog encompassing 4320 viral operational taxonomic units (vOTUs) from six main dominant tick species in China, of which 94.8% have not been found in any other environment. To bridge the knowledge gap in tick DNA virus research and provide a crucial resource platform, we developed the Tick DNA Virus Database. This database includes the vOTUs that are known to cause diseases. Most of the predicted vOTUs are associated with dominant bacterial and archaeal phyla. We identified 105 virus-encoded putative auxiliary metabolic genes (AMGs) that are involved in host metabolism and environmental adaptation, potentially influencing ticks through both top-down and bottom-up mechanisms. The identification of microbial communities and antibiotic resistance in wild tick species suggests that wild ticks are reservoirs of antibiotic resistance and potential spreaders of antibiotic resistance. These findings reveal the potential role of tick viruses in ecosystems, highlighting the importance of monitoring tick microbiomes to address global public health challenges.

Commentary on the proposed Section 10 amendments to the International Code of Nomenclature of Prokaryotes regarding Candidatus names

Amendments were proposed to the International Code of Nomenclature of Prokaryotes (ICNP) in January [Arahal et al. (2024) Int. J Syst. Evol. Microbiol. 74: 006188] that would cause major changes in the treatment of Candidatus names. The amendments introduce Section 10 to name taxa whose names cannot be validly published under the ICNP because of the absence of type strains. This section creates a parallel 'pro-nomenclature' and formalizes alternative material which could serve as nomenclatural types. When conspecific isolates of taxa with Candidatus names are deposited in culture collections as type strains, the names can be validly published, and it is required that the same Candidatus name be used. While the amendments are promoted to provide stable names and rules of nomenclature for uncultivated taxa, the system is deeply flawed. It removes the permanent association between names and types, which will make the meaning of names imprecise and ambiguous. It creates 'pro-nomenclature', which is confusing and unnecessary. Since many taxa which cannot be validly named under the ICNP can already be named under the SeqCode, it duplicates and creates overlap with an established nomenclatural system without providing tangible benefits. As the SeqCode recognizes names formed under the ICNP, the ICNP should recognize names formed under the SeqCode as they have done for the Cyanobacteria named under the International Code of Nomenclature for algae, fungi and plants (ICN). For these reasons, we urge the members of the International Committee of Systematics of Prokaryotes (ICSP) to reject these amendments.

Swimming towards each other: the role of chemotaxis in bacterial interactions

Chemotaxis allows microorganisms to direct movement in response to chemical stimuli. Bacteria use this behaviour to develop spatial associations with animals and plants, and even larger microbes. However, current theory suggests that constraints imposed by the limits of chemotactic sensory systems will prevent sensing of chemical gradients emanating from cells smaller than a few micrometres, precluding the utility of chemotaxis in interactions between individual bacteria. Yet, recent evidence has revealed surprising levels of bacterial chemotactic precision, as well as a role for chemotaxis in metabolite exchange between bacterial cells. If indeed widespread, chemotactic sensing between bacteria could represent an important, but largely overlooked, phenotype within interbacterial interactions, and play a significant role in shaping cooperative and competitive relationships.

Removal of metals and emergent contaminants from liquid digestates in constructed wetlands for agricultural reuse

Given the increasing pressure on water bodies, it is imperative to explore sustainable methodologies for wastewater treatment and reuse. The simultaneous presence of multiples contaminants in complex wastewater, such as the liquid effluents from biogas plants, can compromise biological treatment effectiveness for reclaiming water. Vertical subsurface flow constructed wetlands were established as low-cost decentralized wastewater treatment technologies to treat the liquid fraction of digestate from municipal organic waste with metals, antibiotics, and antibiotic resistance genes, to allow its reuse in irrigation. Twelve lab-scale planted constructed wetlands were assembled with gravel, light expanded clay aggregate and sand, testing four different treating conditions (liquid digestate spiked with oxytetracycline, sulfadiazine, or ofloxacin, at 100 μg/ L, or without dosing) during 3 months. Physicochemical parameters (pH, chemical oxygen demand (COD), nutrients, metals, and antibiotics), the microbial communities dynamics (through 16S high-throughput sequencing) and antibiotic resistance genes removal (qPCR) were monitored in influents and effluents. Systems removed 85.8%-96.9% of organic matter (as COD), over 98.1% of ammonium and phosphate ions, and 69.3%-99.4% of nitrate and nitrite ions, with no significant differences between the presence or absence of antibiotics. Removal of Fe, Mn, Zn, Cu, Pb and Cr exceeded 82% in all treatment cycles. The treatment also removed oxytetracycline, sulfadiazine and ofloxacin over 99%, and decreased intl1, tetA, tetW, sul1 and qnrS gene copies. Nonetheless, after 3 months of ofloxacin dosing, qnrS gene started being detected. Removal processes relied on high HRT (14 days) and various mechanisms including sorption, biodegradation, and precipitation. Microbial community diversity in liquid digestate changed significantly after treatment in constructed wetlands with a decrease in the initial Firmicutes dominance, but with no clear effect of antibiotics on the microbial community structure. Removals above 85% and 94% were observed for Streptococcus and Clostridium, respectively. Results suggest that vertical subsurface flow constructed wetlands were a suitable technology for treating the liquid digestate to reuse it in irrigation agricultural systems, contributing to the circular bioeconomy concept. However, a more profound understanding of effective wastewater treatment strategies is needed to avoid antibiotic resistance genes dissemination.

Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen-deficient zones with diverse metabolic potential

Archaea belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have been found in an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise a sizeable fraction of the archaeal community within marine oxygen-deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes (MAGs) belonging to the DPANN phyla Nanoarchaeota, Pacearchaeota, Woesearchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and the Arabian Sea. We find these archaea to be permanent, stable residents of all three major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25%-50% of archaea as estimated from read mapping to MAGs. ODZ DPANN appear to be capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs.

IMPORTANCE

Archaea from the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have diverse metabolic capabilities and participate in multiple biogeochemical cycles. While metagenomics and enrichments have revealed that many DPANN are characterized by ultrasmall genomes, few biosynthetic genes, and episymbiotic lifestyles, much remains unknown about their biology. We report 33 new DPANN metagenome-assembled genomes originating from the three global marine oxygen-deficient zones (ODZs), the first from these regions. We survey DPANN abundance and distribution within the ODZ water column, investigate their biosynthetic capabilities, and report potential roles in the cycling of organic carbon, methane, and nitrogen. We test the hypothesis that nitrous oxide reductases found within several ODZ DPANN genomes may enable ultrasmall episymbionts to serve as nitrous oxide consumers when attached to a host nitrous oxide producer. Our results indicate DPANN archaea as ubiquitous residents within the anoxic core of ODZs with the potential to produce or consume key compounds.

High niche specificity and host genetic diversity of groundwater viruses

Viruses are key members of microbial communities that exert control over host abundance and metabolism, thereby influencing ecosystem processes and biogeochemical cycles. Aquifers are known to host taxonomically diverse microbial life, yet little is known about viruses infecting groundwater microbial communities. Here, we analysed 16 metagenomes from a broad range of groundwater physicochemistries. We recovered 1571 viral genomes that clustered into 468 high-quality viral operational taxonomic units. At least 15% were observed to be transcriptionally active, although lysis was likely constrained by the resource-limited groundwater environment. Most were unclassified (95%), and the remaining 5% were Caudoviricetes. Comparisons with viruses inhabiting other aquifers revealed no shared species, indicating substantial unexplored viral diversity. In silico predictions linked 22.4% of the viruses to microbial host populations, including to ultra-small prokaryotes, such as Patescibacteria and Nanoarchaeota. Many predicted hosts were associated with the biogeochemical cycling of carbon, nitrogen, and sulfur. Metabolic predictions revealed the presence of 205 putative auxiliary metabolic genes, involved in diverse processes associated with the utilization of the host's intracellular resources for biosynthesis and transformation reactions, including those involved in nucleotide sugar, glycan, cofactor, and vitamin metabolism. Viruses, prokaryotes overall, and predicted prokaryotic hosts exhibited narrow spatial distributions, and relative abundance correlations with the same groundwater parameters (e.g. dissolved oxygen, nitrate, and iron), consistent with host control over viral distributions. Results provide insights into underexplored groundwater viruses, and indicate the large extent to which viruses may manipulate microbial communities and biogeochemistry in the terrestrial subsurface.

Genome-resolved metaproteogenomic and nanosolid characterization of an inactive vent chimney densely colonized by enigmatic DPANN archaea

Recent successes in the cultivation of DPANN archaea with their hosts have demonstrated an episymbiotic lifestyle, whereas the lifestyle of DPANN archaea in natural habitats is largely unknown. A free-living lifestyle is speculated in oxygen-deprived fluids circulated through rock media, where apparent hosts of DPANN archaea are lacking. Alternatively, DPANN archaea may be detached from their hosts and/or rock surfaces. To understand the ecology of rock-hosted DPANN archaea, rocks rather than fluids should be directly characterized. Here, we investigated a deep-sea hydrothermal vent chimney without fluid venting where our previous study revealed the high proportion of Pacearchaeota, one of the widespread and enigmatic lineages of DPANN archaea. Using spectroscopic methods with submicron soft X-ray and infrared beams, the microbial habitat was specified to be silica-filled pores in the inner chimney wall comprising chalcopyrite. Metagenomic analysis of the inner wall revealed the lack of biosynthetic genes for nucleotides, amino acids, cofactors, and lipids in the Pacearchaeota genomes. Genome-resolved metaproteomic analysis clarified the co-occurrence of a novel thermophilic lineage actively fixing carbon and nitrogen and thermophilic archaea in the inner chimney wall. We infer that the shift in metabolically active microbial populations from the thermophiles to the mesophilic DPANN archaea occurs after the termination of fluid venting. The infilling of mineral pores by hydrothermal silica deposition might be a preferred environmental factor for the colonization of free-living Pacearchaeota with ultrasmall cells depending on metabolites synthesized by the co-occurring thermophiles during fluid venting.

Novel candidate taxa contribute to key metabolic processes in Fennoscandian Shield deep groundwaters

The continental deep biosphere contains a vast reservoir of microorganisms, although a large proportion of its diversity remains both uncultured and undescribed. In this study, the metabolic potential (metagenomes) and activity (metatranscriptomes) of the microbial communities in Fennoscandian Shield deep subsurface groundwaters were characterized with a focus on novel taxa. DNA sequencing generated 1270 de-replicated metagenome-assembled genomes and single-amplified genomes, containing 7 novel classes, 34 orders, and 72 families. The majority of novel taxa were affiliated with Patescibacteria, whereas among novel archaea taxa, Thermoproteota and Nanoarchaeota representatives dominated. Metatranscriptomes revealed that 30 of the 112 novel taxa at the class, order, and family levels were active in at least one investigated groundwater sample, implying that novel taxa represent a partially active but hitherto uncharacterized deep biosphere component. The novel taxa genomes coded for carbon fixation predominantly via the Wood-Ljungdahl pathway, nitrogen fixation, sulfur plus hydrogen oxidation, and fermentative pathways, including acetogenesis. These metabolic processes contributed significantly to the total community's capacity, with up to 9.9% of fermentation, 6.4% of the Wood-Ljungdahl pathway, 6.8% of sulfur plus 8.6% of hydrogen oxidation, and energy conservation via nitrate (4.4%) and sulfate (6.0%) reduction. Key novel taxa included the UBA9089 phylum, with representatives having a prominent role in carbon fixation, nitrate and sulfate reduction, and organic and inorganic electron donor oxidation. These data provided insights into deep biosphere microbial diversity and their contribution to nutrient and energy cycling in this ecosystem.

Using Genomics to Decipher the Enigmatic Properties and Survival Adaptation of Candidate Phyla Radiation

Microbial ecology is a critical field for understanding the composition, diversity, and functions of microorganisms in various environmental and health-related processes. The discovery of Candidate Phyla Radiation (CPR) through culture-independent methods has introduced a new division of microbes characterized by a symbiotic/parasitic lifestyle, small cell size, and small genome. Despite being poorly understood, CPRs have garnered significant attention in recent years due to their widespread detection in a variety of environmental and clinical samples. These microorganisms have been found to exhibit a high degree of genetic diversity compared to other microbes. Several studies have shed light on their potential importance in global biogeochemical cycles and their impact on various human activities. In this review, we provide a systematic overview of the discovery of CPRs. We then focus on describing how the genomic characteristics of CPRs have helped them interact with and adapt to other microbes in different ecological niches. Future works should focus on discovering the metabolic capacities of CPRs and, if possible, isolating them to obtain a better understanding of these microorganisms.