Microbiomes in a manganese oxide producing ecosystem in the Ytterby mine, Sweden: impact on metal mobility

Collaborative or competitive interactions between bacteria and methanogens on the biocorrosion of Q235A steel

Bio-corrosion of Fe (0) metals in the actual environments results from the combined action of multiple microbes rather than the single action of one type of microbe. Nevertheless, the interspecies interactions between the corrosive microorganism and co-existing microbes, as well as their effects on the bio-corrosion of Fe (0) metals, remain unclear, especially for the interspecies interactions between methanogens and co-existed bacteria in microbiota in the absence of sulfate. Herein, the interspecies interactions between methanogens and co-existed bacteria in three different kinds of methanogenic microbiota (Methanothrix, Methanospirillum, or Methanobacterium dominant) and their effects on methanogens-influenced corrosion of Q235A steel were investigated. The initial results showed that competitive interactions existed between Methanothrix/Methanospirllum and fermentative acetogenic bacteria (Clostridiaceae_1, Family_XI, Peptostreptococcaceae, Pirllulaceae, and Tannerellaceae), while collaborative interactions existed between Methanobacterium and acetate-oxidizing bacteria (Synergistaceae and Spirochaetaceae). Further analysis demonstrated that the competitive interactions obstructed the attachment of Methanothrix/Methanospirllum and promoted the formation of dense corrosion products layer on the steel surface, thereby inhibiting Methanothrix/Methanospirllum-influenced corrosion. Contrarily, the collaborative interactions promoted the attachment of Methanobacterium and the formation of porous and loose corrosion products layer on the steel surface, thereby promoting Methanobacterium-influenced corrosion. Ultimately, the corrosion rate of steel induced by the Methanobacterium dominant microbiota (0.216 ± 0.042 mm/y) was much higher than by the Methanothrix/Methanospirllum dominant microbiota (0.009-0.046 mm/y). This work provided new insights into the understanding of the effects of co-existed bacteria on the corrosion of Fe (0) metals induced by methanogens in microbiota.

Microbial community analysis of sand filters used to treat mine water from a closed uranium mine

Rapid sand filters (RSFs) are employed in a drinking water treatment to remove undesirable elements such as suspended solids and dissolved metal ions. At a closed uranium (U) mine site, two sets of tandemly linked paired RSF systems (RSF1-RSF2 and RSF1-RSF3) were utilized to remove iron and manganese from mine water. In this study, a 16S rRNA-based amplicon sequencing survey was conducted to investigate the core microbes within the RSF system treating the mine water. In RSF1, two operational taxonomic units (OTUs) related to methanotrophic bacteria, Methylobacter tundripaludum (relative abundance: 18.1%) and Methylovulum psychrotolerans (11.5%), were the most and second most dominant species, respectively, alongside iron-oxidizing bacteria. The presence of these OTUs in RSF1 can be attributed to the microbial community in the inlet mine water, as the three most abundant OTUs in the mine water also dominated RSF1. Conversely, in both RSF2 and RSF3, Nevskia sp., previously isolated from the Ytterby mine manganese oxide producing ecosystem, became dominant, although known manganese-oxidizing bacterial OTUs were not detected. In contrast, a unique OTU related to Rhodanobacter sp. was the third most abundant (8.0%) in RSF1, possibly due to selective pressure from the radionuclide-contaminated environment during RSF operation, as this genus is known to be abundant at nuclear legacy waste sites. Understanding the key bacterial taxa in RSF system for mine water treatment could enhance the effectiveness of RSF processes in treating mine water from closed U mines.

Genomic insights into the alphaproteobacterium Georhizobium sp. MAB10 revealed a pathway of Mn(II) oxidation-coupled anoxygenic photoautotrophy: a novel understanding of the biotic process in deep-sea ferromanganese nodule formation

Under light conditions, Mn(II) facilitates the photoautotrophic growth of Georhizobium sp. MAB10, a strain derived from deep-sea ferromanganese nodules, along with the generation of dark Mn oxides (β-MnO2). This study investigated the genetic basis of Mn(II) oxidation-coupled anoxygenic photoautotrophy using genome sequencing and biochemical assays of strain MAB10. Preliminary results indicated the presence of genes encoding a functional pheophytin-quinone-type photosynthetic reaction center and a putative key enzyme for Mn(II) oxidation, namely FtsP/CotA-like multicopper oxidase GE001273. Under light conditions, Mn(II) significantly reduced the respiration rate and elevated the intracellular NADH/NADtotal ratio. This suggested that Mn(II)-derived electrons entered the cyclic photophosphorylation, partially replacing the oxidative phosphorylation for ATP production and enhancing the electron flow to complex I for NADH generation. In vitro enzymatic studies confirmed that GE001273 was a catalyst for Mn(II) oxidation in the outer membrane. Comprehensive genomic analyses of respiration and carbon and nitrogen metabolism revealed the high ecophysiological flexibility of strain MAB10 during Mn(II) oxidation-coupled anoxygenic photoautotrophy in deep-sea habitats. These analyses provided insights into bacterial Mn(II) oxidation-coupled anoxygenic photoautotrophy during microorganism-mediated deep-sea ferromanganese nodule formation.

IMPORTANCE

Microorganisms are believed to participate in the biotic process of deep-sea ferromanganese nodule formation [Mn(II) oxidation]. Despite the multitude of studies and reviews focusing on the details of Mn(II) oxidation catalyzed by diverse heterotrophs, the mechanistic roles of manganese chemolithotrophs from ferromanganese nodules remain unclear. We demonstrate that strain Georhizobium sp. MAB10 can utilize Mn(II)-derived electrons for photoautotrophic growth, with concomitant generation of dark β-MnO2 type Mn oxides under near-infrared light condition. This study uses genomic and biochemical assays to explore the genetic basis of Mn(II) oxidation-coupled anoxygenic photoautotrophy. The comprehensive analyses of respiration and carbon and nitrogen metabolism further elucidated the high ecophysiological flexibility of strain MAB10 in deep-sea habits. These findings expand our understanding of the role of chemolithotrophs in deep-sea ferromanganese nodule formation and justify further investigations into the molecular basis for Mn(II) oxidation-coupled anoxygenic photoautotrophy.

Biogenic manganese oxides promote metal(loid) remediation by shaping microbial communities in biological aqua crust

Biological aqua crust (biogenic aqua crust-BAC) is a potentially sustainable solution for metal(loid) bioremediation in global water using solar energy. However, the key geochemical factors and underlying mechanisms shaping microbial communities in BAC remain poorly understood. The current study aimed at determining the in situ metal(loid) distribution and the key geochemical factors related to microbial community structure and metal(loid)-related genes in BAC of a representative Pb/Zn tailing pond. Here we showed that abundant metal(loid)s (e.g. Pb, As) were co-distributed with Mn/Fe-rich minerals (e.g. biogenic Mn oxide, FeOOH) in BAC. Biogenic Mn oxide (i.e. Mn) was the most dominant factor in shaping microbial community structure in BAC and source tailings. Along with the fact that keystone species (e.g. Burkholderiales, Haliscomenobacter) have the potential to promote Mn ion oxidization and particle agglomeration, as well as Mn is highly associated with metal(loid)-related genes, especially genes related to As redox (e.g. arsC, aoxA), and Cd transport (e.g. zipB), biogenic Mn oxides thus effectively enhance metal(loid) remediation by accelerating the formation of organo-mineral aggregates in biofilm-rich BAC system. Our study indicated that biogenic Mn oxides may play essential roles in facilitating in situ metal(loid) bioremediation in BAC of mine drainage.

Startup performance and microbial composition of a pilot-scale rapid sand filter for the treatment of manganese-containing mine water

The inexpensive removal of soluble manganese [Mn(II)] from mine water that contains large quantities of Mn(II) should be prioritized given that large quantities of alkaline reagents are typically used in the chemical treatment of Mn-rich water from abandoned mines. Rapid sand filter (RSF) systems are widely used as a cost-effective technology in drinking water treatment processes to remove iron and Mn from groundwater. Here, we applied a pilot-scale RSF to treat mine water with a neutral pH and containing approximately 22 mg/L of Mn(II). Following a lag phase from its startup (day 1-day 26), Mn removal rates increased to approximately 40% for around 1 month (day 27-day 55) without the use of alkaline reagents but did not increase during further operation. Quantitative elemental analysis revealed Mn oxides on the sand filters during the Mn removal period. The bacterial communities on the RSFs, recorded on day 42 and day 85, were characterized and compared using 16S rRNA gene amplicon sequencing. Although the well-known Mn-oxidizing bacteria (MOB) were not listed among the ten most dominant operational taxonomic units (OTUs) on the sand filters (relative abundances: >0.68%), a significant increase in the OTUs related to well-known alphaproteobacterial MOB, such as Pedomicrobium spp., were observed during the period.

Biological Oxygen-dosed Activated Carbon (BODAC) filters - A bioprocess for ultrapure water production removing organics, nutrients and micropollutants

Biological oxygen-dosed activated carbon (BODAC) filters in an Ultrapure water plant were demonstrated to have the potential to further treat secondary wastewater treatment effluent. The BODAC filters were operated for 11 years without carbon regeneration or replacement, while still functioning as pre-treatment step to reverse osmosis (RO) membranes by actively removing organic micropollutants (OMPs) and foulants. In this study, the removal of nutrients and 13 OMPs from secondary wastewater treatment effluent was investigated for 2 years and simultaneously, the granules' characterization and microbial community analysis were conducted to gain insights behind the stable long-term operation of the BODAC filters. The results showed that the BODAC granules' surface area was reduced by ∼70 % of what is in virgin carbon granules and covered by biofilm and inorganic depositions. The BODAC filters reduced the concentration of soluble organics, mainly proteins, performed as an effective nitrification system, and almost completely removed manganese. During the 2 years of observation, the filters consistently removed some OMPs such as hydrochlorothiazide, metoprolol, sotalol, and trimethoprim by at least 70 %. Finally, through microbial community analysis, we found that nitrifying and manganese-oxidizing bacteria were detected in high relative abundance on BODAC granules, supporting BODAC performance in removing OMPs and manganese as well as converting nitrogenous species in the water.

Diversity, distribution and organic substrates preferences of microbial communities of a low anthropic activity cave in North-Western Romania

Introduction

Karst caves are characterized by relatively constant temperature, lack of light, high humidity, and low nutrients availability. The diversity and functionality of the microorganisms dwelling in caves micro-habitats are yet underexplored. Therefore, in-depth investigations of these ecosystems aid in enlarging our understanding of the microbial interactions and microbially driven biogeochemical cycles. Here, we aimed at evaluating the diversity, abundance, distribution, and organic substrate preferences of microbial communities from Peștera cu Apă din Valea Leșului (Leșu Cave) located in the Apuseni Mountains (North-Western Romania).

Materials and Methods

To achieve this goal, we employed 16S rRNA gene amplicon sequencing and community-level physiological profiling (CLPP) paralleled by the assessment of environmental parameters of cave sediments and water.

Results and Discussion

Pseudomonadota (synonym Proteobacteria) was the most prevalent phylum detected across all samples whereas the abundance detected at order level varied among sites and between water and sediment samples. Despite the general similarity at the phylum-level in Leșu Cave across the sampled area, the results obtained in this study suggest that specific sites drive bacterial community at the order-level, perhaps sustaining the enrichment of unique bacterial populations due to microenvironmental conditions. For most of the dominant orders the distribution pattern showed a positive correlation with C-sources such as putrescine, γ-amino butyric acid, and D-malic acid, while particular cases were positively correlated with polymers (Tween 40, Tween 80 and α-cyclodextrin), carbohydrates (α-D-lactose, i-erythritol, D-mannitol) and most of the carboxylic and ketonic acids. Physicochemical analysis reveals that sediments are geochemically distinct, with increased concentration of Ca, Fe, Al, Mg, Na and K, whereas water showed low nitrate concentration. Our PCA indicated the clustering of different dominant orders with Mg, As, P, Fe, and Cr. This information serves as a starting point for further studies in elucidating the links between the taxonomic and functional diversity of subterranean microbial communities.

Genomic Comparisons of Two Armillaria Species with Different Ecological Behaviors and Their Associated Soil Microbial Communities

Armillaria species show considerable variation in ecological roles and virulence, from mycorrhizae and saprophytes to important root pathogens of trees and horticultural crops. We studied two Armillaria species that can be found in coniferous forests of northwestern USA and southwestern Canada. Armillaria altimontana not only is considered as a weak, opportunistic pathogen of coniferous trees, but it also appears to exhibit in situ biological control against A. solidipes, formerly North American A. ostoyae, which is considered a virulent pathogen of coniferous trees. Here, we describe their genome assemblies and present a functional annotation of the predicted genes and proteins for the two Armillaria species that exhibit contrasting ecological roles. In addition, the soil microbial communities were examined in association with the two Armillaria species within a 45-year-old plantation of western white pine (Pinus monticola) in northern Idaho, USA, where A. altimontana was associated with improved tree growth and survival, while A. solidipes was associated with reduced growth and survival. The results from this study reveal a high similarity between the genomes of the beneficial/non-pathogenic A. altimontana and pathogenic A. solidipes; however, many relatively small differences in gene content were identified that could contribute to differences in ecological lifestyles and interactions with woody hosts and soil microbial communities.

Metagenomic evidence of a novel family of anammox bacteria in a subsea environment

Bacteria in the order 'Candidatus Brocadiales' within the phylum Planctomycetes (Planctomycetota) have the remarkable ability to perform anaerobic ammonium oxidation (anammox). Two families of anammox bacteria with different biogeographical distributions have been reported, marine Ca. Scalinduaceae and freshwater Ca. Brocadiaceae. Here we report evidence of three new species within a novel genus and family of anammox bacteria, which were discovered in biofilms of a subsea road tunnel under a fjord in Norway. In this particular ecosystem, the nitrogen cycle is likely fuelled by ammonia from organic matter degradation in the fjord sediments and the rock mass above the tunnel, resulting in the growth of biofilms where anammox bacteria can thrive under oxygen limitation. We resolved several metagenome-assembled genomes (MAGs) of anammox bacteria, including three Ca. Brocadiales MAGs that could not be classified at the family level. MAGs of this novel family had all the diagnostic genes for a full anaerobic ammonium oxidation pathway in which nitrite was probably reduced by a NirK-like reductase. A survey of published molecular data indicated that this new family of anammox bacteria occurs in many marine sediments, where its members presumably would contribute to nitrogen loss.

Rethinking microbial infallibility in the metagenomics era

The 'principle of microbial infallibility' was a mainstay of microbial physiology and environmental microbiology in earlier decades. This principle asserts that wherever there is an energetic gain to be made from environmental resources, microorganisms will find a way to take advantage of the situation. Although previously disputed, this claim was revived with the discovery of anammox bacteria and other major contributors to biogeochemistry. Here, we discuss the historical background to microbial infallibility, and focus on its contemporary relevance to metagenomics. Our analysis distinguishes exploration-driven metagenomics from hypothesis-driven metagenomics. In particular, we show how hypothesis-driven metagenomics can use background assumptions of microbial infallibility to enable the formulation of hypotheses to be tested by enrichment cultures. Discoveries of comammox and the anaerobic oxidation of methane are major instances of such strategies, and we supplement them with outlines of additional examples. This overview highlights one way in which metagenomics is making the transition from an exploratory data-analysis programme of research to a hypothesis-testing one. We conclude with a discussion of how microbial infallibility is a heuristic with far-reaching implications for the investigation of life.

Effect of PAHs on nitrogen-fixing and sulfate-reducing microbial communities in seagrass Enhalus acoroides sediment

Seagrass meadows are vital ecosystems with high productivity and biodiversity and often in the oligotrophic area. Nitrogen usually limits productivity in this ecosystem as the main nutrient factor. Biological nitrogen fixation by diazotrophs in the rhizosphere sediment can introduce "new" nitrogen into the ecosystem. Previous studies revealed that most sulfate-reducing bacteria (SRB) can also fix nitrogen like the nitrogen-fixing bacteria (NFB). Moreover, both sulfate reduction and nitrogen fixation were affected by the organic pollutant. However, rare information is available regarding the NFB and SRB community composition and their temporal response to the pollutant. The quantitative real-time polymerase chain reaction and polymerase chain reaction denaturing gradient gel electrophoresis have been used to analyze NFB and SRB communities' shifts under different PAHs concentrations. They both experienced a dramatic shift under PAHs stress but exhibited different patterns. SRB could use the low and high concentration PAHs at the early stage of the incubation, while only the low concentration of PAHs could stimulate the growth of NFB through the whole incubation period. The predominant species of NFB communities were Alphaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria; while for SRB communities were class Epsilonproteobacteria. Redundancy analysis indicated the significant environmental factors for the two communities were both ammonium and pH (P < 0.05). There existed nifH sequences related to known nitrogen fixing SRB Desulfatibacillum alkenivorans, which confirmed that microbial N₂ fixation and sulfate reduction were coupled in the seagrass ecosystem by molecular technique. Our investigation provides new insight into the NFB and SRB community in the seagrass meadow.