Autotrophic Microbes Research Articles

Microplastics alter the functioning of marine microbial ecosystems

AbstractMicroplastics pervade ocean ecosystems. Despite their effects on individuals or populations are well documented, the consequences of microplastics on ecosystem functioning are still largely unknown. Here, we show how microplastics alter the structure and functioning of pelagic microbial ecosystems. Using experimental pelagic mesocosms, we found that microplastics indirectly affect marine productivity by changing the bacterial and phytoplankton assemblages. Specifically, the addition of microplastics increased phytoplankton biomass and shifted bacterial assemblages' composition. Such changes altered the interactions between heterotrophic and autotrophic microbes and the cycling of ammonia in the water column, which ultimately benefited photosynthetic efficiency. The effects of microplastics on marine productivity were consistent for different microplastic types. This study demonstrates that microplastics affect bacteria and phytoplankton communities and influence marine productivity, which ultimately alters the functioning of the whole ocean ecosystem.

Effects of additives on compost quality and cbbL-containing autotrophic microbial community of watermelon straw composting

The amount of CO2 emission reflects the microbial activity in compost, but excessive emission can reduce humification degree of compost. Therefore, this study assessed the effects of superphosphate (SSP) and dicyandiamide (DCD) on CO2 emission, compost quality, and cbbL-containing autotrophic microbes (CCAM) community of watermelon straw composting. Results revealed that SSP and DCD promoted the compost maturity, but the DCD alone did not significant effect of the compost. Single DCD (T1) reduced CO2 emission by 7.02 % and increased humic acid content by 3.09 %. DCD+SSP (T2) resulted in a 15.26 % reduction in CO2 emission, a 9.13 % increase in humic acid content, and a significant increase in compost humification level. Furthermore, DCD+SSP improved the abundance and diversity of the CCAM (mainly Proteobacteria and Actinobacteria), improved the compost microenvironment and reduced carbon loss by 6.89 %. Redundancy analysis (RDA) showed that CCAM community had strong correlations with TOC (84.8 %). This study results provided theoretical and practical support for further exploring the carbon emission reduction in composting and promoting sustainable agricultural development.

Microbial Autotrophy Recorded by Carbonate Dual Clumped Isotope Disequilibrium

AbstractThe proliferation of microbial carbon fixation is a key control on the evolution of the biosphere and global carbon cycle. Most records of these metabolisms in ancient rocks come from organic matter or fossils, which are not always preserved. Here, we present a potential proxy for microbial carbon fixation (autotrophy) based on the isotopic composition of carbonate minerals. Autotrophs influence carbonate chemistry in the cellular microenvironment by decreasing CO2 concentration and increasing the carbonate saturation state. This can induce rapid precipitation of carbonate minerals that are out of isotopic equilibrium with their environment. Recent work has identified disequilibrated dual clumped isotope compositions (∆47 and ∆48) in the skeletal fossils of marine calcifying organisms. Here we test whether the same is true of non‐skeletal carbonate fabrics associated with microbial autotrophs in modern and Eocene lakes. We found that microbial carbonate formed via autotrophic metabolism recorded lower ∆47 and higher ∆48 values (−∆47/+∆48) than predicted for thermodynamic equilibrium mineral formation. Our findings are supported by models of dual clumped isotope kinetics in the DIC system, and disequilibrium in the oxygen isotope system. We hypothesize that the inverse trajectory away from the equilibrium line (+∆47/−∆48) should be recorded by carbonates formed in association with alkalinizing heterotrophs, such as sulfate reducers. If so, carbonate dual clumped isotopes could be a powerful tool to identify the proliferation and rate of heterotrophic and autotrophic metabolisms in the carbonate rock record on Earth and (perhaps) other planets.

Overview of the research work of Dr. Hui-Ping Chuang

Dr Hui-Ping Chuang, Sustainable Environment Research Laboratories, National Cheng Kung University, Taiwan, is investigating the ability of different environmental microorganisms to degrade pollutants and produce sustainable resources. A particular focus is on the microbes involved in the nitrogen cycle. She collaborates with Japanese researchers at DHS Technology, Hiroshima University and Tohoku University, among others, as well as communicating with Taiwan researchers based at National Taiwan University and National Chiayi University. Chuang is currently involved in five studies: exploring different types of sponge media for cultivating slow-growing functional microbes; investigating aerobic autotrophic microbes for the conversion of greenhouse potential (GHP) gases such as N2O and CO2 to mitigate global warming; investigating the application of different functional microbes for treating different types of wastewaters containing nitrogenous compounds or alkylphenol compounds or long-term alkanes; cultivating a chloroethane-degrading community used for remediation of soil and groundwater pollution; exploring the use of an anaerobic microbial community for the treatment of biological waste to produce the green energy as methane (CH4) and nitrogen fertiliser as resources; and developing a microbial monitoring platform integrating chemical and molecular analyses. This microbial monitoring platform can be used to detect and quantify nitrogen oxidising or reducing microorganisms, as well as other groups with some modifications and it has now been used in various fields to understand important relationships.

Artificial Soil-Like Material Enhances CO2 Bio-Valorization into Chemicals in Gas Fermentation.

Gas fermentation offers a carbon-neutral route for producing industrial feedstocks using autotrophic microbes to convert carbon dioxide (CO2) in waste gases, such as industrial emissions and biogas, into valuable chemicals or biofuels. However, slow microbial metabolism owing to low gaseous solubility causes significant challenges in gas fermentation. Although chemical or genetic manipulations have been explored to improve gas fermentation, they are either nonsustainable or complex. Herein, an artificial soil-like material (SLM) inspired by natural soil was fabricated to improve the growth and metabolism ofCupriavidus necatorfor enhanced poly-β-hydroxybutyrate (PHB) biosynthesis from CO2 and hydrogen (H2). Porous SLM comprises low-cost nanoclay, boehmite, and starch and serves as a biocarrier to facilitate the colonization of bacteria and delivery of CO2 to bacteria. With 3.0 g/L SLM addition, the solubility of CO2 in water increased by ∼4 times and biomass and PHB production boosted by 29 and 102%, respectively, in the 24 h culture. In addition, a positive modulation was observed in the metabolism of PHB biosynthesis. PHB biosynthesis-associated gene expression was found to be enhanced in response to the SLM addition. The concentrations of intermediates in the metabolic pathway of PHB biosynthesis, such as pyruvate and acetyl-CoA, as well as reducing energy (ATP and NADPH) significantly increased with SLM addition. SLM also demonstrated the merits of easy fabrication, high stability, recyclability, and plasticity, thereby indicating its considerable potential for large-scale application in gas fermentation.

Autotrophic production of polyhydroxyalkanoates using acidogenic-derived H2 and CO2 from fruit waste

The environmental concerns regarding fossil plastics call for alternative biopolymers such as polyhydroxyalkanoates (PHAs) whose manufacturing costs are however still too elevated. Autotrophic microbes like Cupriavidus necator, able to convert CO2 and H2 into PHAs, offer an additional strategy. Typically, the preferred source for CO2 and H2 are expensive pure gases or syngas, which has toxic compounds for most PHAs-accumulating strains. In this work, for the first time, H2 and CO2 originating from an acidogenic reactor were converted autotrophically into poly(3-hydroxybutyrate) P(3HB). During the first stage, a mixed microbial community continuously catabolized melon waste into H2 (26.7 %) and CO2 (49.2 %) that were then used in a second bioreactor by C. necator DSM 545 to accumulate 1.7 g/L P(3HB). Additionally, the VFAs (13 gCOD/L) produced during acidogenesis were processed into 2.7 g/L of P(3HB-co-3HV). This is the first proof-of-concept of using acidogenic-derived H2 and CO2 from fruit waste to produce PHAs.

The effect of polyvinyl chloride (PVC) color on biofilm development and biofilm-heavy metal chemodynamics in the aquatic environment

Plastic surfaces are colonized by microorganisms and biofilms are formed in the natural aquatic environment. As the biofilm develops, it changes the density and buoyancy of the plastic-biofilm complex, results in plastic sinking, and increases the heavy metals accumulated by biofilm's mobility and availability in aquatic ecosystems. In this experiment, biofilms were cultured on five colors of polyvinyl chloride (PVC; transparent, green, blue, red, black) in an aquatic environment to investigate the effects of plastic color on biofilm formation and development (Phase 1) and to study the effects of being sunk below the photic zone on biofilm (Phase 2). The PVC color significantly affected the biofilm formation rate but had no impact on the final biofilm biomass. After sinking the biofilm-PVC below the photic zone in Phase 2, the layer of diatoms on the biofilm surface began to disintegrate, and the biomass and Chlorophyll-a (Chla) content of the biofilm decreased, except on the red PVC. Below the photic zone, the microbial community of the biofilm changed from primarily autotrophic microbes to mostly heterotrophic microbes. Microbial diversity increased and extracellular polymeric substances (EPS) content decreased. The primary factor leading to microbial diversity and community structure changes was water depth rather than PVC color. The changes induced in the biofilm led to an increase in the concentration of all heavy metals in the biofilm, related to the increase in microbial diversity. This study provides new insights into the biofilm formation process and the effects on a biofilm when it sinks below the photic zone.

Effects of different land-use types on the activity and community of autotrophic microbes in karst soil

CO2 fixation by soil autotrophic microbes could make considerable contribution to soil organic matter (SOM). However, the effects of different land-use types on the activity and community of soil autotrophic microbes are still unclear. In this study, the autotrophic carbon fixation (ACF) rates of karst soils with four land-use types were assessed by 13CO2 labelling. After 21 days incubation under alternate 12 h light with darkness, the ACF rate was 0.18 mg C·kg-1·day-1 in bare land soil, approximately 0.39 mg C·kg-1·day-1 in crop land and shrub land soils, while sharply increased to 1.54 mg C·kg−1·day−1 in grass land soil. The 13C nuclear magnetic resonance analysis of SOM showed that the fixed 13CO2 was mainly incorporated into carbonyl carbon in grass land soil, but largely incorporated into recalcitrant aromatic carbon in other land-use types, especially in bare land. Longer incubation time (21 days versus 7 days) greatly elevated ACF rate only in grass land soil (by about 4 times) under continuous light conditions, suggesting that longer incubation in light conditions largely stimulated microbial phototrophic CO2 fixation in grass land soil. Metagenomic analysis showed that the soil autotrophic microbial communities were prominently different among the four land-use types, and the autotrophic populations using bicarbonate as inorganic carbon species were most important for explaining the variations of autotrophic communities among the land-use types. Additionally, total nitrogen and soil organic carbon contents could be the key controlling factors of both ACF rates and structure of autotrophic microbial communities. Eventually, the change of soil properties caused by land-use type substantially affected the activity and community of soil autotrophic microbes, as well as the fate and stability of the assimilated CO2.

Core autotrophic microbes drive functional stability of soil cbbL-containing autotrophic microbes during desertification

The desertification process is characterized by the degradation of soil habitats and attenuation of plant biomass, leading to decreased soil carbon (C) input and increased environmental stress gradients of soil microbes. C dioxide assimilation driven through autotrophic microorganisms is the main process of soil C cycling, and the ecological role of autotrophic microbes is critical for soil C sequestration. However, the feedback dynamics of autotrophic microbes and their functional activity in soil profiles during desertification have not been explored. Here, we analysed three typical stages of desertification (potential, moderate and severe desertification) by high-throughput sequencing and enzyme activity assays to investigate the variation trends of autotrophic microbes and the maintenance of C fixation activity along soil profiles (0–100 cm) as desertification proceeded. We found that the desertification process reduced the abundance and diversity of autotrophic microbes, but increased the activity of soil microbial C fixation enzymes, which highlights the importance of microbial CO2 fixation in oligotrophic soil profiles in desert ecosystems. In particular, we demonstrated that core autotrophic microbes drove the compositional difference of autotrophic microbes, which in turn affected soil C fixation activity, suggesting that core autotrophic microbes are critical for maintaining C sequestration during desertification. Taken together, these results strengthen our comprehension of the factors driving soil functional stability and emphasize that core microbes should be viewed as pivotal factors in maintaining functional activity and ecosystem sustainability during desertification.

Land use differentially alters microbial interactions and detritivore feeding during leaf decomposition in headwater streams

Abstract Human‐driven land conversion from forest to agriculture introduces nutrients, like nitrogen (N) and phosphorus (P), which upon entering nearby streams can stimulate growth and metabolism of microbial autotrophs (algae) and heterotrophs (fungi and bacteria). Recent evidence indicates that algae also can stimulate microbial heterotrophs associated with decaying plant litter by exuding labile carbon (C), defined as the priming effect on decomposition. These autotroph–heterotroph interactions may further alter detritivore feeding ecology, suggesting many complex mechanisms of land‐use change on stream ecosystem functions. In order to investigate the effects of land use on autotroph–heterotroph interactions, we used a full‐factorial design manipulating labile C (glucose and acetate) and nutrients (N and P) to test their effects during red maple litter decomposition within four forested and four pasture agriculture streams in the Point Remove catchment, Arkansas. We deployed nutrient‐diffusing substrates (NDS) containing litter and either agar, agar + labile C, agar + NP, or agar + CNP for 20 days and measured microbial biomass and metabolism, and detrital mass loss. Additionally, we fed litter to Tipula sp. to assess shifts in consumption and egestion rates. Both microbial heterotrophs and autotrophs responded to NDS manipulations, but not land use. Heterotrophic microbes showed evidence of nutrient limitation and negative priming, while algal biomass was negatively associated with heterotrophs. Tipula consumption and egestion rates were both elevated when feeding on litter incubated in agriculture streams, but only egestion responded to NDS manipulations, suggesting a change in assimilation efficiencies. Cumulatively, we suggest that altered stream conditions, such as those resulting from land‐use change, can alter food webs and detritivore feeding more heavily than microbial interactions during litter decomposition in stream ecosystems. These results add to the literature demonstrating shifts in autotroph–heterotroph interactions with anthropogenic nutrient pollution, and the implications for detritivore feeding and overall C cycling in streams.

Environmental impacts of microplastic and role of plastisphere microbes in the biodegradation and upcycling of microplastic

Increasing usage of plastic has led to the deposition of plastic in the environment which later become microplastic, a pollutant of global concern. These polymeric particles affect the ecosystem by increasing ecotoxicity and impeding the biogeochemical cycles. Besides, microplastic particles have been known for their role in aggravating the effect of various other environmental pollutants including organic pollutants and heavy metals. These microplastic surfaces are often colonized by the microbial communities also known as “plastisphere microbes” forming biofilms. These microbes include cyanobacteria like Nostoc, Scytonema, etc., and diatoms like Navicula, Cyclotella, etc. which become the primary colonizer. In addition to the autotrophic microbes, Gammaproteobacteria and Alphaproteobacteria dominate the plastisphere microbial community. These biofilm-forming microbes can efficiently degrade the microplastic in the environment by secreting various catabolic enzymes such as lipase, esterase, hydroxylase, etc. Besides, these microbes have shown great potential for the bioconversion of microplastic to polyhydroxyalkanoates (PHA), an energy efficient and sustainable alternative to the petroleum based plastics. Thus, these microbes can be used for the creation of a circular economy using waste to wealth strategy. This review provides a deeper insight into the distribution, transportation, transformation, and biodegradation of microplastic in the ecosystem. The formation of plastisphere by the biofilm-forming microbes has been described in the article. In addition, the microbial metabolic pathways and genetic regulations involved in the biodegradation have been discussed in detail. The article suggests the microbial bioremediation and upcycling of microplastic along with various other strategies to effectively mitigate the microplastic pollution.

Dose effect of pig manure addition on cbbL-harboring bacterial community in a paddy soil

CO2 fixation by autotrophic microbes has a significant effect on C cycle in agricultural filed. Organic fertilization is an eco-friendly strategy for environmental protection and agricultural sustainability via ameliorating soil microbial community. However, the information of the dose effect of organic fertilizer on soil CO2 fixing microbes has been less documented. In this study, the cbbL gene, a key gene in the Calvin-Benson-Bassham cycle, was used to characterize the CO2-fixing microbes under the gradient rates of pig manure (PM) addition (0, 1400, 2800, 5600, 11,200, 22,400, and 44,800 kg ha−1) in a 5-year field experiment with a double-rice cropping system in the red soil region of China. The results showed that Proteobacteria and Actinobacteria accounted for ∼99.4 % of total cbbL-harboring bacteria in average. High PM doses (22,400 and 44,800 kg ha−1), rather than Low PM doses (11,200 kg ha−1 and less), would significantly change the cbbL-harboring bacterial community attributes. Specifically, high PM doses decreased the alpha-diversity of cbbL-harboring bacterial community and the relative abundances of some lineages belonging to Proteobacteria and Actinobacteria, such as Bradyrhizobium Methylibium, and Variovorax, but increased the proportions of some stress-tolerant taxa (i.e. Hydrogenophaga and Methyloferula). Redundancy analysis (RDA) and partial least squares path modeling (PLS-PM) showed that pH, AP, and metals (Cu and Zn) negatively influenced the cbbL-harboring bacterial diversity and components through PM addition. Collectively, our study demonstrated that high PM addition would potentially threaten the soil cbbL-harboring microbes, and a rational application of manure-derived organic fertilizer should be addressed in agriculture for maintaining soil bio-diversity in future.

Ambient temperature CO2 fixation to pyruvate and subsequently to citramalate over iron and nickel nanoparticles

The chemical reactions that formed the building blocks of life at origins required catalysts, whereby the nature of those catalysts influenced the type of products that accumulated. Recent investigations have shown that at 100 °C awaruite, a Ni3Fe alloy that naturally occurs in serpentinizing systems, is an efficient catalyst for CO2 conversion to formate, acetate, and pyruvate. These products are identical with the intermediates and products of the acetyl-CoA pathway, the most ancient CO2 fixation pathway and the backbone of carbon metabolism in H2-dependent autotrophic microbes. Here, we show that Ni3Fe nanoparticles prepared via the hard-templating method catalyze the conversion of H2 and CO2 to formate, acetate and pyruvate at 25 °C under 25 bar. Furthermore, the 13C-labeled pyruvate can be further converted to acetate, parapyruvate, and citramalate over Ni, Fe, and Ni3Fe nanoparticles at room temperature within one hour. These findings strongly suggest that awaruite can catalyze both the formation of citramalate, the C5 product of pyruvate condensation with acetyl-CoA in microbial carbon metabolism, from pyruvate and the formation of pyruvate from CO2 at very moderate reaction conditions without organic catalysts. These results align well with theories for an autotrophic origin of microbial metabolism under hydrothermal vent conditions.

Effects of emergent plants on soil carbon-fixation and denitrification processes in freshwater and brackish wetlands in a watershed in northern China

Plants could affect wetland ecosystem functions by influencing the carbon and nitrogen cycles driven by microorganisms. However, the underlying mechanisms associated with CO2-fixation rate (CFR) by autotrophic microbes and denitrification rate (DR) in relation to wetland emergent plants remain unclear. In this study, we conducted a field experiment to analyze the effects of emergent plants on the activities and community characteristics of CO2-fixing autotrophic bacteria and denitrifying bacteria in two types of wetlands in a lake basin: freshwater and brackish water. We found that the effects of emergent plants on CFR and DR differed between freshwater and brackish wetlands. Compared to freshwater wetland, brackish wetland exhibited higher CFR in the rhizosphere, probably due to the abundance of organic carbon conducive to facultative autotrophic bacteria. However, the lower rhizosphere DR in brackish wetland compared to that in freshwater wetland was due to the salt stress. In both freshwater and brackish wetlands, rhizosphere soil increased CFR and DR. The microbial communities associated with them were distinct from those in non-rhizosphere. Besides, neutral-based processes governed the assembly of these bacterial communities, while the rhizosphere showed more prominent dominance of niche-based processes than non-rhizosphere. Statistical analyses revealed that soil organic carbon and root exudates jointly drove the differences in the metabolic activities and composition of CO2-fixation- and denitrification-associated microbial communities between rhizosphere and non-rhizosphere. Overall, our findings suggest that the organic carbon released by plants through root exudates and plant litter is vital for promoting wetland soil carbon-fixation and denitrification and alleviating the detrimental effects of salinity on denitrification. This study provides valuable information for the conservation of CO2-fixation and nitrogen removal with suitable plant species in wetlands.

Microbial autotrophy explains large-scale soil CO2 fixation.

Microbial communities play critical roles in fixing carbon from the atmosphere and fixing it in the soils. However, the large-scale variations and drivers of these microbial communities remain poorly understood. Here, we conducted a large-scale survey across China and found that soil autotrophic organisms are critical for explaining CO2 fluxes from the atmosphere to soils. In particular, we showed that large-scale variations in CO2 fixation rates are highly correlated to those in autotrophic bacteria and phototrophic protists. Paddy soils, supporting a larger proportion of obligate bacterial and protist autotrophs, display four-fold of CO2 fixation rates over upland and forest soils. Precipitation and pH, together with key ecological clusters of autotrophic microbes, also played important roles in controlling CO2 fixation. Our work provides a novel quantification on the contribution of terrestrial autotrophic microbes to soil CO2 fixation processes at a large scale, with implications for global carbon regulation under climate change.

Impacts of Co-application of Chemical Fertilizer Reduction and Organic Material Amendment on Fluvo-aquic Soil Microbial N-cycling Functional Gene Abundances and N-converting Genetic Potentials in Northern China

The emerging environment-associated issues due to the overuse of inorganic fertilizers in agricultural production are of global concern despite the benefit of high yields. Eco-friendly organic materials with the capability to fertilize soil are encouraged to partially replace mineral fertilizer. The N cycle conducted by soil microorganisms is the most important biogeochemical process, dictating the N bioavailability in farmland ecosystems; however, little is known about how organic material amendment affects soil microbial N cycling under chemical fertilizer reduction. Hence, a fixed field trial with five fertilization practices was implemented to experimentally alter microorganisms essential for the soil N cycle, including conventional chemical fertilization (NPK), reduced chemical fertilization (NPKR), reduced chemical fertilization plus straw (NPKRS), reduced chemical fertilization plus organic fertilizer (NPKRO), and reduced chemical fertilization plus organic fertilizer and straw (NPKROS). The microbial N-cycling gene abundances and associated N-converting genetic potentials were evaluated using real-time quantitative PCR. In comparison to conventional chemical fertilization (NPK), organic addition significantly increased the amounts of heterotrophic microbes involved in organic N decomposition, N fixation, and N reduction; however, it reduced autotrophic microbes performing ammonia oxidization. Consequently, the overall proportion of heterotrophic microbes was remarkably enhanced, and the autotrophic proportion was correspondingly lowered. The fertilization practice shift significantly improved N fixation and gaseous N emission potentials, whereas it suppressed NO3- leaching potential. A significant discrepancy among five fertilization treatments was observed based on functional gene abundances (PERMANOVA, P=0.002),as revealed by distance-based redundancy analysis (db-RDA), with NH4+ as the dominant factor. Organic fertilizer addition was beneficial for heterotrophic N functional microorganisms, with simultaneous input of straw augmenting such an effect. Pearson's correlation analysis revealed that N storage and gaseous N emission potentials were both substantially negatively correlated with NH4+; NO3- leaching potential was notably negatively associated with SOC and TN but significantly related to NH4+. In conclusion, chemical fertilizer reduction combined with organic material amendments, a main fertilization recommendation, may enhance soil N storage, diminish N loss by leaching, and mitigate the environmental risk of N2O emission. This deserves attention considering that healthy and sustainable agricultural soil environment can be cultivated from the view of microbial N-cycling.

Chemotaxonomic patterns in intracellular metabolites of marine microbial plankton

Most biological diversity on Earth is contained within microbial communities. In the ocean, these communities dominate processes related to carbon fixation and nutrient recycling. Yet, specific factors that determine community composition and metabolic activity are difficult to resolve in complex microbial populations, complicating predictions of microbial processes in a changing ocean. Microbial metabolism generates small organic molecules that reflect both the biochemical and physiological diversity as well as the taxonomic specificity of these biological processes. These small molecules serve as the conduit for taxon-specific signaling and exchange. Here, we use liquid chromatography-mass spectrometry (LC-MS)-based metabolomics to taxonomically categorize 111 metabolites that include small molecules in central and secondary metabolism across 42 taxa representing numerically dominant and metabolically important lineages of microbial autotrophs and heterotrophs. Patterns in metabolite presence-absence broadly reflected taxonomic lineages. A subset of metabolites that includes osmolytes, sulfur-containing metabolites, sugars, and amino acid derivatives provided chemotaxonomic information among phytoplankton taxa. A variety of phytohormones and signaling molecules were predominantly found in the heterotrophic bacteria and archaea, expanding knowledge of metabolites implicated in modulating interactions between microbes. This chemotaxonomic inventory of marine microbial metabolites is a key step in deciphering metabolic networks that influence ocean biogeochemical cycles.

Community characteristics of autotrophic CO2-fixing bacteria in karst wetland groundwaters with different nitrogen levels.

Karst wetlands are important in the global carbon and nitrogen cycles as well as in security of water resources. Huixian wetland (Guilin) is the largest natural karst wetland in China. In recent years, groundwater nitrogen pollution has increasingly affected the wetland ecosystem integrity due to anthropogenic activities. In this study, it was hypothesized that autotrophic microbial diversity is impacted with the advent of pollution, adversely affecting autotrophs in the carbon and nitrogen cycles. Autotrophic microbes have important roles in abating groundwater nitrogen pollution. Thus, it is of great significance to study the characteristics of autotrophic bacterial communities and their responses to environmental parameters in nitrogen-polluted karst groundwaters. The abundances of the Calvin–Benson cycle functional genes cbbL and cbbM as well as the autotrophic CO2-fixing bacterial communities were characterized in the karst groundwater samples with different levels of nitrogen pollution. The cbbM gene was generally more abundant than the cbbL gene in the groundwater samples. The cbbL gene abundance was significantly positively correlated with dissolved inorganic nitrogen (DIN) concentration (P < 0.01). In the autotrophic CO2-fixing bacterial communities, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria of the phylum Proteobacteria were predominant. At the genus level, Rubrivivax and Methylibium were the dominant cbbL gene containing genera, while Halothiobacillus and Endothiovibrio were the dominant genera for the cbbM gene. The abundance of autotrophic CO2-fixing bacterial communities increased but their diversity decreased with the inflow of nitrogen into the karst groundwater system. The community structure of autotrophic CO2-fixing bacteria in the groundwaters was also significantly affected by environmental factors such as the carbonic anhydrase (CA) activity, dissolved inorganic carbon (DIC) concentration, temperature, and oxidation-reduction potential (ORP). Nitrogen inflow significantly changed the characteristics of autotrophic CO2-fixing bacterial communities in the karst groundwaters. Some key genera such as Nitrosospira and Thiobacillus were clearly abundant in the karst groundwaters with high nitrogen levels. Their respective roles in nitrification and denitrification impact nitrogen removal in this ecosystem. The findings in this study provide an important reference for biological abatement of nitrogen pollution in the karst groundwater system.

Effect of electric current intensity on performance of polycaprolactone/FeS2-based mixotrophic biofilm–electrode reactor

In this study, a bioelectrochemical system consisting of pyrite-based autotrophic denitrification (PAD) and heterotrophic denitrification (HD) was established to polish nitrate wastewater. The loading of electric current (EC) could stimulate the dissolution of pyrite. Appropriate EC (I ≤ 30 mA) was conducive to nitrate removal, too high EC (I = 40 mA) would inhibit nitrate removal and lead to an obvious accumulation of NO2–-N and NH4+-N. Microbial analysis revealed that the increase of EC could inhibit the diversity of heterotrophic microbes, but appropriate EC (I = 10 mA) could increase the diversity of autotrophic microbes. The EC loading was conducive to the enrichment of iron autotrophic denitrifiers (Ferritrophicum), pyrite-oxidizing bacteria (Thiobacillus, Sulfurimonas), and sulfur autotrophic denitrifiers (Dechloromonas, Thiobacillus, and Arenimonas). The EC loading enlarged the contribution of PAD, making PAD a dominant pathway in denitrification.

Fluxes of the Amazon River plume nutrients and microbes into marine sponges

Sponges have co-evolved with microbes for over 400 myr. Previous studies have demonstrated that sponges can be classified according to the abundance of microbes in their tissues as Low Microbial Abundance (LMA) and High Microbial Abundance (HMA). While LMA sponges rely mainly on water column microbes, HMA appear to rely much more on symbiotic fermentative and autotrophic microbes maintained in their tissues. However, it is unclear if this pattern holds when comparing different species of tropical sponges under extreme nutrient conditions and sediment loads in the water column, such as the Great Amazon Reef System (GARS), which covers an area of ~56,000 km2 off the Amazon River mouth. Sponges are the major GARS benthic components. However, these sponges' microbiome across the GARS is still unknown. Here, we investigated water quality, isotopic values (δ13C and δ15N), metagenomic and lipidomic profiles of sponges obtained from different sectors throughout the GARS. >180 million shotgun metagenomic reads were annotated, covering 22 sponge species. Isotopic and lipidomic analyses suggested LMA sponges rely on the Amazon River Plume for nutrition. HMA sponges (N = 15) had higher Roseiflexus and Nitrospira abundance, whereas LMA sponges (N = 7) had higher Prochlorococcus and Pelagibacter abundance. Functional data revealed that the LMA sponge microbiomes had greater number of sequences related to phages and prophages as well as electron transport and photophosphorylation which may be related to photosynthetic processes associated with the Prochlorococcus and Synechococcus found in the LMA. The higher phages abundance in LMA sponges could be related to these holobionts' reduced defense towards phage infection. Meanwhile, HMA sponge microbiomes had higher Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR abundance, which may be involved in defense against phage infection. This study sheds light on the nutrient fluxes and microbes from the Amazon River plume into the sponge holobionts.