Effects of the Hydroxy-Regulated Li-Montmorillonite Atomic Interface Arrangement on Li Cycle of Marine Sedimentation and pH.

The reaction of ubiquitous clay is related to the global cycle of the key metals, but the relationship between the Li occurrence interface and the sedimentation in the Li cycle remains unclear. We investigated the atomic interface arrangement of Li-montmorillonite (Li-Mt) during low-temperature water-rock reactions and Li migration. The results show that, in Cl-rich systems, deprotonation and exposure of Na adsorption sites cause Li enrichment and O pairing, which lead to the weakening of the shielding effect of Mt on anions and the formation of a Mt-Li-Cl atomically interfacial arrangement. Only up to 20.3% of the Li is contained in the atomic interface of Li-Mt. In F-rich system, the dehydroxylation of F paired with Al in octahedral sites causes Li accumulation via local crystallization of LiF, and co-complexation of F and Li forms a Mt(Al)-F-Li atomic interface, in which up to 46.8% of the Li is enriched by the Mt. The participation of F and Cl in the complexation intensifies lattice collapse of the Li-Mt edge. The sedimentation velocity decreases with the smaller particle size affected by the Li loading. Lithium leached from igneous rocks serves as the marine Li source, which contributes up to 99.8% and 99.5% of the Li in Cl- and F-rich systems, respectively. The response of Mt(OH) to Li migration with a time accumulating effect may make an important regulatory of oceanic pH by either acidification or alkalization.

Mechanisms of Lithium Enrichment and Metallogenesis in a Simulated Montmorillonite-Fluid System.

Due to strong industrial demand for Li, Li-bearing montmorillonite (Li-Mt) deposits are a focus for exploration, but the Li enrichment mechanisms in such deposits are unclear. In this study, adsorption experiments and mineralogical analyses were used to investigate the water-rock reactions at different Li concentrations, temperatures, durations, and pH conditions, in order to reveal the Li enrichment mechanisms in F- and Cl-rich systems. Our results suggest that water-rock reactions are different in the two halogen systems. The reaction in the LiCl-Mt system involves deprotonation, whereas dehydroxylation occurs in a LiF-Mt system. Lithium is adsorbed or exchanges with interlayer cations in Mt. Adsorption forms a monolayer that is consistent with the Langmuir model in a LiCl system. Lithium is adsorbed in multi-layers in Mt in a LiF system. For a given Li concentration, the adsorption capacity of the LiF-Mt system is 2.8 times greater than that of the LiCl-Mt system. The pH has a weaker effect in the LiCl-Mt system than in the LiF-Mt system. Furthermore, Li adsorption is hindered at very high or low pH in a LiF system. The chemical shift of Li is -0.2 ppm (±0.1 ppm) in a nuclear magnetic resonance (NMR), which indicates that Li occurs as inner-sphere complexes in the pseudo-hexagonal cavity in Mt. Based on a CaCl2 leaching experiment, >50% (up to 97.94%) of the Li can be easily exchanged out of the Mt. The residual Li in the inner-sphere is the key to metallogenesis of Li-Mt deposits. Therefore, the grade of ion adsorption-type Li deposits is determined by the exchangeable Li.

Effect of Stoichiometry on Nanomagnetite Sulfidation.

Magnetite (Mt) has long been regarded as a stable phase with a low reactivity toward dissolved sulfide, but natural Mt with varying stoichiometries (the structural Fe(II)/Fe(III) ratio, xstru) might exhibit distinct reactivities in sulfidation. How Mt stoichiometry affects its sulfidation processes and products remains unknown. Here, we demonstrate that xstru is a master variable controlling the rates and extents of sulfide oxidation by magnetite nanoparticles (11 ± 2 nm). At pH = 7.0-8.0 and the initial Fe/S molar ratio of 10-50, the partially oxidized magnetite (xstru = 0.19-0.43) can oxidize dissolved sulfide to elemental sulfur (S0), but only surface adsorption of sulfide, without interfacial electron transfer (IET), occurs on the nearly stoichiometric magnetite (xstru = 0.47). The higher initial rate and extent of sulfide oxidation and S0 production are observed with the more oxidized magnetite that has the higher electron-accepting capability from surface-complexed sulfide (S(-II)(s)). The FeS clusters formed from magnetite sulfidation can be oxidized by the most oxidized magnetite with xstru = 0.19 but not by other magnetite particles. A linear relationship between the Gibbs free energy of reaction and the surface area-normalized initial rate of sulfide oxidation is observed in all experiments under the different conditions, suggesting the S(-II)(s)-magnetite IET dominates magnetite sulfidation at high Fe/S molar ratios and near-neutral pH.

Gene expression in the microbial consortia of colonial Microcystis aeruginosa-a potential buoyant particulate biofilm.

Microcystis spp., notorious bloom-forming cyanobacteria, are often present in colony form in eutrophic lakes worldwide. Uncovering the mechanisms underlying Microcystis colony formation and maintenance is vital to controlling the blooms, but it has long been a challenge. Here, bacterial communities and gene expression patterns of colonial and unicellular forms of one non-axenic strain of Microcystis aeruginosa isolated from Lake Taihu were compared. Evidently, different microbial communities between them were observed through 16S rDNA MiSeq sequencing. Metatranscriptome analyses revealed that transcripts for pathways involved in bacterial biofilm formation, such as biosynthesis of peptidoglycan and arginine by Bacteroidetes, methionine biosynthesis, alginate metabolism, flagellum, and motility, as well as widespread colonization islands by Proteobacteria, were highly enriched in the colonial form. Furthermore, transcripts for nitrogen fixation and denitrification pathways by Proteobacteria that usually occur in biofilms were significantly enriched in the colonial Microcystis. Results revealed that microbes associated with Microcystis colonies play important roles through regulation of biofilm-related genes in colony formation and maintenance. Moreover, Microcystis colony represents a potential 'buoyant particulate biofilm', which is a good model for biofilm studies. The biofilm features of colonial Microcystis throw a new light on management and control of the ubiquitous blooms in eutrophic waters.

Revealing the community and metabolic potential of active methanotrophs by targeted metagenomics in the Zoige wetland of the Tibetan Plateau.

The Zoige wetland of the Tibetan Plateau is one of the largest alpine wetlands in the world and a major emission source of methane. Methane oxidation by methanotrophs can counteract the global warming effect of methane released in the wetlands. Understanding methanotroph activity, diversity and metabolism at the molecular level can guide the isolation of the uncultured microorganisms and inform strategy-making decisions and policies to counteract global warming in this unique ecosystem. Here we applied DNA stable isotope probing using 13 C-labelled methane to label the genomes of active methanotrophs, examine the methane oxidation potential and recover metagenome-assembled genomes (MAGs) of active methanotrophs. We found that gammaproteobacteria of type I methanotrophs are responsible for methane oxidation in the wetland. We recovered two phylogenetically novel methanotroph MAGs distantly related to extant Methylobacter and Methylovulum. They belong to type I methanotrophs of gammaproteobacteria, contain both mxaF and xoxF types of methanol dehydrogenase coding genes, and participate in methane oxidation via H4 MPT and RuMP pathways. Overall, the community structure of active methanotrophs and their methanotrophic pathways revealed by DNA-SIP metagenomics and retrieved methanotroph MAGs highlight the importance of methanotrophs in suppressing methane emission in the wetland under the scenario of global warming.

Atmospheric Methane Oxidizers Are Dominated by Upland Soil Cluster Alpha in 20 Forest Soils of China.

Upland soil clusters alpha and gamma (USCα and USCγ) are considered a major biological sink of atmospheric methane and are often detected in forest and grassland soils. These clusters are phylogenetically classified using the particulate methane monooxygenase gene pmoA because of the difficulty of cultivation. Recent studies have established a direct link of pmoA genes to 16S rRNA genes based on their isolated strain or draft genomes. However, whether the results of pmoA-based assays could be largely represented by 16S rRNA gene sequencing in upland soils remains unclear. In this study, we collected 20 forest soils across China and compared methane-oxidizing bacterial (MOB) communities by high-throughput sequencing of 16S rRNA and pmoA genes using different primer sets. The results showed that 16S rRNA gene sequencing and the semi-nested polymerase chain reaction (PCR) of the pmoA gene (A189/A682r nested with a mixture of mb661 and A650) consistently revealed the dominance of USCα (accounting for more than 50% of the total MOB) in 12 forest soils. A189f/A682r successfully amplified pmoA genes (mainly RA14 of USCα) in only three forest soils. A189f/mb661 could amplify USCα (mainly JR1) in several forest soils but showed a strong preferential amplification of Methylocystis and many other type I MOB groups. A189f/A650 almost exclusively amplified USCα (mainly JR1) and largely discriminated against Methylocystis and most of the other MOB groups. The semi-nested PCR approach weakened the bias of A189f/mb661 and A189f/A650 for JR1 and balanced the coverage of all USCα members. The canonical correspondence analysis indicated that soil NH4+-N and pH were the main environmental factors affecting the MOB community of Chinese forest soils. The RA14 of the USCα group prefers to live in soils with low pH, low temperature, low elevation, high precipitation, and rich in nitrogen. JR1's preferences for temperature and elevation were opposite to RA14. Our study suggests that combining the deep sequencing of 16S rRNA and pmoA genes to characterize MOB in forest soils is the best choice.

Community Structure of Active Aerobic Methanotrophs in Red Mangrove (Kandelia obovata) Soils Under Different Frequency of Tides.

Methanotrophs are important microbial communities in coastal ecosystems. They reduce CH4 emission in situ, which is influenced by soil conditions. This study aimed to understand the differences in active aerobic methanotrophic communities in mangrove forest soils experiencing different inundation frequency, i.e., in soils from tidal mangroves, distributed at lower elevations, and from dwarf mangroves, distributed at higher elevations. Labeling of pmoA gene of active methanotrophs using DNA-based stable isotope probing (DNA-SIP) revealed that methanotrophic activity was higher in the dwarf mangrove soils than in the tidal mangrove soils, possibly because of the more aerobic soil conditions. Methanotrophs affiliated with the cluster deep-sea-5 belonging to type Ib methanotrophs were the most dominant methanotrophs in the fresh mangrove soils, whereas type II methanotrophs also appeared in the fresh dwarf mangrove soils. Furthermore, Methylobacter and Methylosarcina were the most important active methanotrophs in the dwarf mangrove soils, whereas Methylomonas and Methylosarcina were more active in the tidal mangrove soils. High-throughput sequencing of the 16S ribosomal RNA (rRNA) gene also confirmed similar differences in methanotrophic communities at the different locations. However, several unclassified methanotrophic bacteria were found by 16S rRNA MiSeq sequencing in both fresh and incubated mangrove soils, implying that methanotrophic communities in mangrove forests may significantly differ from the methanotrophic communities documented in previous studies. Overall, this study showed the feasibility of 13CH4 DNA-SIP to study the active methanotrophic communities in mangrove forest soils and revealed differences in the methanotrophic community structure between coastal mangrove forests experiencing different tide frequencies.

[Research progress of atmospheric methane oxidizers in soil].

Microbial oxidation in soil is the only biological sink for atmospheric methane (about 1.8 ppmv). Two groups of atmospheric methane oxidizing bacteria are existed in aerobic soils: obligate and alternative atmospheric methane oxidizing bacteria. The former, such as upland soil cluster alpha (USCalpha) and upland soil cluster gamma (USCgamma), are widely distributed in a variety of aerobic upland soils, and their particulate methane monooxygenase (pMMO) have very high affinity for methane in low concentration. Bacteria in this group are probably genuine oligotrophs. However, so far, there is still no cultivated strain of this group. The latter (Methylocystis/Methylosinus) belongs to traditional methane-oxidizing bacteria, and are widely distributed in soil environments with periodic high methane emission. Most strains of these two genera are known to possess two pMMO isozymes with low and high affinity to methane respectively, and these strains can keep atmospheric methane oxidizing activity for relative long periods ( > 3 months) relying on the high affinity pMMO (pMMO2). However, the growth and reproduction of bacteria in this group are still dependent on endogenous high-concentration methane which is periodically produced within the soils. We reviewed the research progress of these two groups of atmospheric methane-oxidizing bacteria, their possible living strategies, and the effects of several key environmental factors (e. g. soil temperature and moisture, soil pH, vegetation, land use, nitrogen input) on their community composition and methane oxidizing activity. Several important research directions of atmospheric methane oxidizing bacteria have also been proposed.

[Microbial metabolism in typical flooded paddy soils ].

[OBJECTIVE] The object of this study is to reveal the composition of active microorganism and their metabolic activities in flooded paddy soils with long-term fertilization ( Mineral nitrogen, phosphorus, and potassium, NPK) and without fertilizer (Control check, CK) by environmental transcriptomics. [METHODS] Flooded soil microcosms were incubated in the laboratory for two weeks, then total RNA were extracted from the soil for transcriptome sequencing. Resulting fastq files were uploaded to the Metagenomics Analysis Server (MG-RAST) for taxonomic analysis, gene annotation and function classification. [RESULTS] Transcripts from diverse active microorganism, including bacteria ( > 95% ) , archaea, eukaryotes and viruses, were detected in both flooded paddy soils of CK and NPK treatments. Most of the transcripts (active genes) of bacteria and archaea were derived from Proteobacteria (more than 50% of total bacterial transcripts) and Thaumarchaaeota (about 70% of total archaeal transcripts ) respectively in both treatments. Transcriptional activity of Acidobacteria in NPK treatment paddy soil was significantly higher than that in CK treatment paddy soil. As for other phyla of bacteria and archaea, there were no significant differences of transcriptional activity of them between CK and NPK treatment paddy soils. The highest expressed gene in both CK and NPK treatment paddy soils is ABC transporter encoding gene which related to the transmembrane transport of substances. Based on gene function category of COG (Clusters of Orthologous Genes), Subsystem and KEGG (Kyoto Encyclopedia of Genes and Genomes) database, we found that the main metabolic activities of microorganisms in both CK and NPK treatment paddy soils were related to energy production and conversion, carbohydrate metabolism, protein metabolism and amino acid metabolism, and the dominant KEGG pathways were oxidative phosphorylation and aminoacyl-tRNA biosynthesis. [ CONCLUSION] Composition of active microorganism in CK and NPK treatment paddy soils was generally similar, except Acidobacteria whose transcriptional activity was significantly different between these two treatment paddy soils. It was also very similar between CK and NPK treatment paddy soils considering the metabolic activities of microorganisms in them, for dominant metabolic processes in these two soils were both related to energy obtaining and protein metabolism. So, dominant metabolic activities of microorganism in flooded paddy soils used in this study were not altered significantly under long - term inorganic fertilization.

Ridge with no-tillage facilitates microbial N2 fixation associated with methane oxidation in rice soil.

Aerobic methane-oxidizing bacteria (MOB) play a crucial role in mitigating the greenhouse gas methane emission, particularly prevalent in flooded wetlands. The implementation of ridge with no-tillage practices within a rice-rape rotation system proves effective in overcoming the restrictive redox conditions associated with waterlogging. This approach enhances capillary water availability from furrows, especially during periods of low rainfall, thereby supporting plant growth on the ridges. However, the microbe-mediated accumulation of soil organic carbon and nitrogen remains insufficiently understood under this agricultural practice, particularly concerning methane oxidation, which holds ecological and agricultural significance in the rice fields. In this study, the ridge and ditch soils from a 28-year-old ridge with no-tillage rice field experiment were utilized for incubation with 13C-CH4 and 15NN2 to estimate the methane-oxidizing and N2-fixing potentials. Our findings reveal a significantly higher net production of fresh soil organic carbon in the ridge compared to the ditch soil during methane oxidation, with values of 626 and 543 µg 13C g-1 dry weight soil, respectively. Additionally, the fixed 15N exhibited a twofold increase in the ridge soil (14.1 µg 15N g-1 dry weight soil) compared to the ditch soil. Interestingly, the result of DNA-based stable isotope probing indicated no significant differences in active MOB and N2 fixers between ridge and ditch soils. Both Methylocystis-like type II and Methylosarcina/Methylomonas-like type I MOB catalyzed methane into organic biomass carbon pools. Soil N2-fixing activity was associated with the 15N-labeling of methane oxidizers and non-MOB, such as methanol oxidizers (Hyphomicrobium) and conventional N2 fixers (Burkholderia). Methane oxidation also fostered microbial interactions, as evidenced by co-occurrence patterns. These results underscore the dual role of microbial methane oxidation - not only as a recognized sink for the potent greenhouse gas methane but also as a source of soil organic carbon and bioavailable nitrogen. This emphasizes the pivotal role of microbial methane metabolism in contributing to soil carbon and nitrogen accumulation in ridge with no-tillage systems.

MAPRS: An intelligent approach for post-prescription review based on multi-label learning.

Antimicrobial resistance (AMR) is a major threat to public health worldwide. It is a promising way to improve appropriate prescription by the review and stewardship of antimicrobials, and Post-Prescription Review (PPR) is currently the main tool used in hospitals. Existing methods of PPR typically focus on the dichotomy of antimicrobial prescription based on binary classification which, however, is usually a multi-label classification problem. Moreover, previous research did not explain the causes beneath the inappropriate antimicrobial used in the clinical setting, which could be practically important for problem location and decision improvement. In this paper, we collected antimicrobial prescriptions and related data from clean surgery in a hospital in northeastern China, and proposed a Multi-label Antimicrobial Post-Prescription Review System (MAPRS). MAPRS first uses NLP techniques to process unstructured data in prescriptions and explores the value of clinical record text for solving medical problems. Then, Classifier Chains are used to deal with multi-label problems and fused with machine learning algorithms to construct a classifier. At last, a SHAP explanation module is introduced to explain the inappropriate prescriptions. The experimental results show that MAPRS could achieve great performance in a challenging six-category multi-label task, with a subset accuracy of 90.7 % and an average AUROC of 94.3 %. Our results can help hospitals to perform intelligent prescription review and improve the antimicrobial stewardship.

Identifying Active Rather than Total Methanotrophs Inhabiting Surface Soil Is Essential for the Microbial Prospection of Gas Reservoirs.

Methane-oxidizing bacteria (MOB) have long been recognized as an important bioindicator for oil and gas exploration. However, due to their physiological and ecological diversity, the distribution of MOB in different habitats varies widely, making it challenging to authentically reflect the abundance of active MOB in the soil above oil and gas reservoirs using conventional methods. Here, we selected the Puguang gas field of the Sichuan Basin in Southwest China as a model system to study the ecological characteristics of methanotrophs using culture-independent molecular techniques. Initially, by comparing the abundance of the pmoA genes determined by quantitative PCR (qPCR), no significant difference was found between gas well and non-gas well soils, indicating that the abundance of total MOB may not necessarily reflect the distribution of the underlying gas reservoirs. 13C-DNA stable isotope probing (DNA-SIP) in combination with high-throughput sequencing (HTS) furthermore revealed that type II methanotrophic Methylocystis was the absolutely predominant active MOB in the non-gas-field soils, whereas the niche vacated by Methylocystis was gradually filled with type I RPC-2 (rice paddy cluster-2) and Methylosarcina in the surface soils of gas reservoirs after geoscale acclimation to trace- and continuous-methane supply. The sum of the relative abundance of RPC-2 and Methylosarcina was then used as specific biotic index (BI) in the Puguang gas field. A microbial anomaly distribution map based on the BI values showed that the anomalous zones were highly consistent with geological and geophysical data, and known drilling results. Therefore, the active but not total methanotrophs successfully reflected the microseepage intensity of the underlying active hydrocarbon system, and can be used as an essential quantitative index to determine the existence and distribution of reservoirs. Our results suggest that molecular microbial techniques are powerful tools for oil and gas prospecting.

A kinetics-coupled multi-surface complexation model deciphering arsenic adsorption and mobility across soil types.

The diversity of soil adsorbents for arsenic (As) and the often-overlooked influence of manganese (Mn) on As(III) oxidation impose challenges in predicting As adsorption in soils. This study uses Mössbauer spectroscopy, X-ray diffraction of oriented clay, and batch experiments to develop a kinetic coupled multi-surface complexation model that characterizes As adsorbents in natural soils and quantifies their contributions to As adsorption. The model integrates dynamic adsorption behaviors and Mn-oxide interactions with unified thermodynamic and kinetic parameters. The results indicate that As adsorption is governed by five primary adsorbents: poorly crystalline Fe oxides, well crystalline Fe oxides, Fe-rich clay, Fe-depletion clay, and organic carbon (OC). Fe oxides dominate As adsorption at low As concentrations. However, at higher As concentrations, soils from carbonate strata, with higher content of Fe-rich clay, exhibit stronger As adsorption capabilities than soils from Quaternary sediment strata. The enrichment in Fe-rich clay can enhance the resistance of adsorbed As to reduction processes affecting Fe oxides. Additionally, extensive redox cycles in paddy fields increase OC levels, enhancing their As adsorption compared to upland fields. This model framework provides novel insights into the intricate dynamics of As within soils and a versatile tool for predicting As adsorption across diverse soils.

Spatial heterogeneity of cyanobacterial communities and genetic variation of microcystis populations within large, shallow eutrophic lakes (Lake Taihu and Lake Chaohu, China).

Cyanobacteria, specifically Microcystis, usually form massive blooms in eutrophic freshwater lakes. Cyanobacterial samples were collected from eight sites of both Lake Taihu and Lake Chaohu in late summer to determine the diversity and distribution pattern of cyanobacteria and Microcystis in large, shallow, entropic lakes with significant spatial heterogeneity and long-term Microcystis bloom. Molecular methods based on denaturing gradient gel electrophoresis and clone library analysis were used. A similar heterogeneous distribution pattern of cyanobacteria in both lakes was observed. Most parts of these two lakes with high trophic level were dominated by Microcystis. However, in the regions with low trophic levels as well as low concentrations of chlorophyll a, Synechococcus occupied a considerable percentage. Different morphospecies and genotypes dominated the bloom-forming Microcystis populations in these two lakes. Microcystis viridis and Microcystis novacekii were dominant in Lake Chaohu, whereas Microcystis flos-aquae was dominant in Lake Taihu. Only 2 of thel3 Microcystis operational taxonomic units were shared between these two lakes. Analysis of molecular variance based on 16S to 23S internal transcribed spacer sequences indicated the significAnt genetic differentiation of Microcystis between these two lakes (F(ST) = 0.19, p < 0.001). However, only 19.46% of the genetic variability was explained by the population variation between lakes, whereas most (80.54%) of the genetic variability occurred within the lakes. Phylogenetic analysis revealed no phylogeographic structure of Microcystis population in these two lakes, as illustrated by their cosmopolitan nature. Our results revealed that spatial heterogeneity within lakes has more impact on the cyanobacterial diversity than geographical isolation in a local scale.

Phylogeny and Metabolic Potential of the Methanotrophic Lineage MO3 in Beijerinckiaceae from the Paddy Soil through Metagenome-Assembled Genome Reconstruction.

Although the study of aerobic methane-oxidizing bacteria (MOB, methanotrophs) has been carried out for more than a hundred years, there are many uncultivated methanotrophic lineages whose metabolism is largely unknown. Here, we reconstructed a nearly complete genome of a Beijerinckiaceae methanotroph from the enrichment of paddy soil by using nitrogen-free M2 medium. The methanotroph labeled as MO3_YZ.1 had a size of 3.83 Mb, GC content of 65.6%, and 3442 gene-coding regions. Based on phylogeny of pmoA gene and genome and the genomic average nucleotide identity, we confirmed its affiliation to the MO3 lineage and a close relationship to Methylocapsa. MO3_YZ.1 contained mxaF- and xoxF-type methanol dehydrogenase. MO3_YZ.1 used the serine cycle to assimilate carbon and regenerated glyoxylate through the glyoxylate shunt as it contained isocitrate lyase and complete tricarboxylic acid cycle-coding genes. The ethylmalonyl-CoA pathway and Calvin-Benson-Bassham cycle were incomplete in MO3_YZ.1. Three acetate utilization enzyme-coding genes were identified, suggesting its potential ability to utilize acetate. The presence of genes for N2 fixation, sulfur transformation, and poly-ß-hydroxybutyrate synthesis enable its survival in heterogeneous habitats with fluctuating supplies of carbon, nitrogen, and sulfur.

Methanotrophy Alleviates Nitrogen Constraint of Carbon Turnover by Rice Root-Associated Microbiomes.

The bioavailability of nitrogen constrains primary productivity, and ecosystem stoichiometry implies stimulation of N2 fixation in association with carbon sequestration in hotspots such as paddy soils. In this study, we show that N2 fixation was triggered by methane oxidation and the methanotrophs serve as microbial engines driving the turnover of carbon and nitrogen in rice roots. 15N2-stable isotope probing showed that N2-fixing activity was stimulated 160-fold by CH4 oxidation from 0.27 to 43.3 µmol N g-1 dry weight root biomass, and approximately 42.5% of the fixed N existed in the form of 15N-NH4 + through microbial mineralization. Nitrate amendment almost completely abolished N2 fixation. Ecophysiology flux measurement indicated that methane oxidation-induced N2 fixation contributed only 1.9% of total nitrogen, whereas methanotrophy-primed mineralization accounted for 21.7% of total nitrogen to facilitate root carbon turnover. DNA-based stable isotope probing further indicated that gammaproteobacterial Methylomonas-like methanotrophs dominated N2 fixation in CH4-consuming roots, whereas nitrate addition resulted in the shift of the active population to alphaproteobacterial Methylocystis-like methanotrophs. Co-occurring pattern analysis of active microbial community further suggested that a number of keystone taxa could have played a major role in nitrogen acquisition through root decomposition and N2 fixation to facilitate nutrient cycling while maintaining soil productivity. This study thus highlights the importance of root-associated methanotrophs as both biofilters of greenhouse gas methane and microbial engines of bioavailable nitrogen for rice growth.

Gene expression pattern of microbes associated with large cyanobacterial colonies for a whole year in Lake Taihu.

Large cyanobacterial colonies, which are unique niches for heterotrophic bacteria, are vital for blooming in eutrophic waters. However, the seasonal dynamics of molecular insights into microbes in these colonies remain unclear. Here, the community composition and metabolism pattern of microbes inhabiting large cyanobacterial colonies (> 120 µm, collected from Lake Taihu in China) were investigated monthly. The community structure of total microbes was mostly influenced by chlorophyll a (Chl a), total phosphorus (TP) concentration, dissolved oxygen, and temperature, whereas the colony-associated bacteria (excluding Cyanobacteria) were mostly influenced by total organic carbon, NO3-, and PO43- concentrations, indicating different response patterns of Cyanobacteria and the associated bacteria to water nutrient conditions. Metatranscriptomic data suggested that similar to that of Cyanobacteria, the gene expression patterns of the most active bacteria, such as Proteobacteria and Bacteroidetes, were not strictly dependent on season but separated by Chl a concentrations. Samples in July and September (high-bloom period) and February and March (non-bloom period) formed two distinct clusters, whereas those of other months (low-bloom period) clustered together. The accumulation of transcripts for pathways, such as phycobilisome from Cyanobacteria and bacterial chemotaxis and flagellum, phosphate metabolism, and sulfur oxidation from Proteobacteria, was enriched in high- and low-bloom periods than in non-bloom period. Network analyses revealed that Cyanobacteria and Proteobacteria exhibited coordinated transcriptional patterns in almost all divided modules. Modules had Cyanobacteria-dominated hub gene were positively correlated with temperature, Chl a, total dissolved phosphorus, and NH4+ and NO2- concentrations, whereas modules had Proteobacteria-dominated hub gene were positively correlated with TP and PO43-. These results indicated labor division might exist in the colonies. This study provided metabolic insights into microbes in large cyanobacterial colonies and would support the understanding and management of the year-round cyanobacterial blooms.

Two-stage fluid pathways generated by volume expansion reactions: insights from the replacement of pyrite by chalcopyrite.

Volume expansion reactions involved in mineral-fluid interactions are linked to a number of geological processes, including silicate weathering, retrograde metamorphism, and mineralization. However, the effect of volume expansion on replacement reactions remains unclear. Here, we demonstrate that reactions associated with volume expansion during the replacement of pyrite by chalcopyrite involve two competing processes. The reaction is initially augmented because of the development of reaction-induced fractures in the pyrite. However, these fractures are subsequently filled by compacted products, which ultimately disrupts the contact and interaction between bulk fluids and the pristine pyrite surface. These competing processes indicate that replacement reactions are both augmented and inhibited by volume expansion reactions during pyrite replacement.

Niche Differentiation of Active Methane-Oxidizing Bacteria in Estuarine Mangrove Forest Soils in Taiwan.

Mangrove forests are one of the important ecosystems in tropical coasts because of their high primary production, which they sustain by sequestering a substantial amount of CO2 into plant biomass. These forests often experience various levels of inundation and play an important role in CH4 emissions, but the taxonomy of methanotrophs in these systems remains poorly understood. In this study, DNA-based stable isotope probing showed significant niche differentiation in active aerobic methanotrophs in response to niche differentiation in upstream and downstream mangrove soils of the Tamsui estuary in northwestern Taiwan, in which salinity levels differ between winter and summer. Methylobacter and Methylomicrobium-like Type I methanotrophs dominated methane-oxidizing communities in the field conditions and were significantly 13C-labeled in both upstream and downstream sites, while Methylobacter were well adapted to high salinity and low temperature. The Type II methanotroph Methylocystis comprised only 10-15% of all the methane oxidizers in the upstream site but less than 5% at the downstream site under field conditions. 13C-DNA levels in Methylocystis were significantly lower than those in Type I methanotrophs, while phylogenetic analysis further revealed the presence of novel methane oxidizers that are phylogenetically distantly related to Type Ia in fresh and incubated soils at a downstream site. These results suggest that Type I methanotrophs display niche differentiation associated with environmental differences between upstream and downstream mangrove soils.

Phylogenetic diversity and specificity of bacteria associated with Microcystis aeruginosa and other cyanobacteria.

Interactions between bacteria and cyanobacteria have been suggested to have a potential to influence harmful algal bloom dynamics; however, little information on these interactions has been reported. In this study, the bacterial communities associated with five strains of Microcystis aeruginosa, three species of other Microcystis spp., and four representative species of non-Microcystis cyanobacteria were compared. Bacterial 16S rDNA fragments were amplified and separated by denaturing gradient gel electrophoresis (DGGE) followed by DNA sequence analysis. The similarities among bacterial communities associated with these cyanobacteria were compared to the digitized DGGE profiles using the cluster analyses. The bacterial community structure of all cyanobacterial cultures differed. Cluster analysis showed that the similarity values among M. aeruginosa cultures were higher than those of other cyanobacterial cultures. Sequence analysis of DGGE fragments indicated the presence of bacteria including, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Bacteroidetes and Actinobacteria in the cyanobacterial cultures. Members of the Sphingomonadales were the prevalent group among the Microcystis-associated bacteria. The results provided further evidence for species-specific associations between cyanobacteria and heterotrophic bacteria, which are useful for understanding interactions between Microcystis and their associated bacteria.