Publications

4527

AbstractPurple sulfur bacteria (PSB) of the family Chromatiaceae (Gammaproteobacteria) can perform chemo‐ and photo‐lithoautotrophy (through anoxygenic photosynthesis) in anoxic layers of freshwater stratified (including meromictic) lakes. This group has been extensively studied via physiological and ecological approaches, albeit their genomics has lagged behind. Here, we monitored a small, shallow, karstic lake, Lagunillo de Cardenillas, that developed a pink coloration throughout the whole water column and prevailed for ca. 2 years across seasons of the limnological cycle. Combining the study of physical/chemical parameters, amplicon sequencing, metagenomics, genomics, and microscopy, we observed this phenomenon was caused by blooms of a novel Thiocapsa species, which represented ca. 40% of the total microbial biomass of the lake's water column during the autumn/winter mixing period, and ca. 36% in the anoxic layers during spring/summer stratification. The dominance of this microbe was attributed to the high sulfur concentrations and biogeochemical features of the lake combined with various genomic footprints/abilities of this microbe to utilize different nutrient sources under anoxic and oxic/microaerophilic conditions. The latter included nitrogen (cyanate and ethanolamine hydrolysis, N fixation, dissimilatory nitrate reduction, ammonia assimilation, denitrification), carbon (anoxygenic photosynthesis and the presence of α‐carboxysomes and type IA RuBisCOs) and sulfur (dimethylsulfide [DMS] and thiosulfate oxidation, dimethylsulfoxide [DMSO] reduction). In addition, this novel species possessed genes for gas vesicle formation, anoxic/oxic respiration pathways, hydrogenases, oxic stress response, and a CRISPR‐Cas array. Thus, its extensive genomic repertoire helped explain its versatility and success in colonizing both the anoxic layers and the oxic/anoxic interphase in this lake.

Abstract Aim Candidatus Methanoperedens-related archaea have recently been identified as anaerobic methane oxidizers in paddy soils. Fertilization practices, including the application of inorganic and organic fertilizers (e.g. chicken manure), may significantly influence their community dynamics and the associated methane cycling processes. However, the comparative effects of inorganic and chicken manure fertilization on these archaeal community in paddy fields remain unclear. This study aimed to examine the diversity, community composition, and abundance of Methanoperedens-related archaea at three representative soil layers of 0–10, 20–30, and 40–50 cm under three fertilization treatments (no fertilizer, inorganic fertilizer, chicken manure fertilizer). Methods and results High-throughput sequencing revealed significant differences in community composition among treatments, while overall diversity showed minimal changes. Quantitative Polymerase Chain Reaction indicated that archaeal abundance under inorganic (2.3 × 106 copies g−1) and chicken manure fertilization (2.2 × 106 copies g−1) treatments was significantly greater than that under no fertilization (1.8 × 106 copies g−1) in upper 30 cm soils, with no significant difference at 40–50 cm depth. Inorganic fertilization more strongly promoted archaeal abundance, whereas chicken manure had a greater effect on community structure. Soil ammonium, nitrate, and organic carbon contents were significantly correlated with archaeal community patterns. Conclusion Both inorganic and organic fertilization can substantially influence the community structure and abundance of Methanoperedens-related archaea in paddy soils.

Ticks spread pathogens that affect both human and animal health and often cause significant economic losses to the livestock industry. However, there is limited data on the distribution of ticks and tick-borne pathogens, particularly those affecting cattle in Cameroon. In this study, ticks were collected from cattle in Buea, the capital of the South West Region of Cameroon, to determine their diversity and identify tick-borne pathogens through PCR and sequencing. The tick samples were screened for pathogens using assays that target the rOmpA gene (ompA) of Rickettsia, the ssrRNA gene of Babesia and Theileria and the Ehrlichia genus 16SrRNA gene. A total of 458 ticks were collected with Rhipicephalus annulatus (65.6%) as the predominant species. From 68 tick pools screened, 26 (38.2%) were positive for pathogen/ symbiont DNA. The pathogen identified was Rickettsia africae (22.1%). This study reports the first molecular detection of the symbiont Candidatus Midichloria mitochondrii (22.1%) in the sampled tick species. It was observed that male ticks were significantly more likely to test positive for R. africae (OR = 208, 95% CI = 28.6 - 4553, p<0.001). Animal handlers may face the risk of these zoonotic infections and as such, there is a need to employ protective measures to prevent or reduce pathogen spread.

Abstract The CRISPR–Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated protein) systems are adaptive immune mechanisms that play critical roles in defending archaea and bacteria against invading entities. These systems can be divided into two classes, with class 2 comprising three types (II, V, and VI). Because of their ability to cleave double-stranded DNA, many class 2 CRISPR–Cas proteins have been harnessed as genome editing tools. Unlike the well-studied type II Cas9 proteins, the structural studies of the type V-B Cas12b proteins are limited, hindering their engineering and broader application. Here, we report four complex structures of ChCas12b, which reveal many unique structural features. The folding of the single guide RNA (sgRNA) of ChCas12b is distinct from that of AacCas12b and BthCas12b. Notably, many of these unique features are involved in ChCas12b–sgRNA interaction, suggesting that they are co-evolved. While ChCas12b shares a conserved two-cation-assisted catalytic mechanism with its homologs, it recognizes a longer guide:target heteroduplex, potentially offering higher fidelity in DNA editing. Altogether, our studies suggested that Cas12b family proteins exhibit significant diversity in their folding, sgRNA and target DNA binding. In the future, it is worth characterizing more representative proteins to identify CRISPR–Cas proteins with higher gene editing ability and fidelity.

Despite their large environmental impact and multiple independent emergences, the processes leading to the evolution of anaerobic methanotrophic archaea (ANME) remain unclear. This work uses comparative metagenomics of a recently evolved but understudied ANME group, “ Candidatus Methanovorans” (ANME-3), to identify evolutionary processes and innovations at work in ANME, which may be obscured in earlier evolved lineages. We identified horizontal transfer of hdrA homologs and convergent evolution in carbon and energy metabolic genes as potential early steps in Methanovorans evolution. We also identified the erosion of genes required for methylotrophic methanogenesis along with horizontal acquisition of multiheme cytochromes and other loci uniquely associated with ANME. The assembly and comparative analysis of multiple Methanovorans genomes offers important functional context for understanding the niche-defining metabolic differences between methane-oxidizing ANME and their methanogen relatives. Furthermore, this work illustrates the multiple evolutionary modes at play in the transition to a globally important metabolic niche.