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Bacillus velezensis M3-1 strain isolated from the sediment of Myriophyllum aquatium constructed wetlands was found to efficiently convert NO 3 −-N to NO 2 −-N, and the requirements for carbon source addition were not very rigorous. This work demonstrates, for the first time, the feasibility of using the synergy of anammox and Bacillus velezensis M3-1 microorganisms for nitrogen removal. In this study, the possibility of M3-1 that converted NO 3 −-N produced by anammox to NO 2 −-N was verified in an anaerobic reactor. The NO 3 −-N reduction ability of M3-1 and denitrifying bacteria in coupling system was investigated under different C/N conditions, and it was found that M3-1 used carbon sources preferentially over denitrifying bacteria. By adjusting the ratio of NH 4 +-N to NO 2 −-N, it was found that the NO 2 −-N converted from NO 3 −-N by M3-1 participated in the original anammox.The nitrogen removal efficacy (NRE) of the coupled system was increased by 12.1%, compared to the control group anammox system at C/N = 2:1. Functional gene indicated that it might be a nitrate reducing bacterium.This study shows that the nitrate reduction rate achieved by the Bacillus velezensis M3-1 can be high enough for removing nitrate produced by anammox process, which would enable improve nitrogen removal from wastewater. [ABSTRACT FROM AUTHOR]

Dissolved organic carbon (DOC) released from submerged leaf litter is an important allochthonous carbon source for heterotrophic bacteria that enhances the detrital food chain in freshwater ecosystems. In contrast, nitrogen (N), phosphorus (P) and micronutrients released during the leaching process support primary production and enhance the grazing food chain in these ecosystems.This study investigated how DOC and dissolved N and P from the leaf litter of two temperate broadleaf and two coniferous tree species affect heterotrophic and autotrophic biomass by incubating the freshwater microbial community in the culture media prepared from the leaf litter leachate.The results showed that heterotrophic biomass, including bacteria, heterotrophic‐flagellated protists and fungal zoospores, was the highest in the leaf litter leachate, which contained the highest DOC concentration relative to dissolved N and P (Japanese hemlock). In contrast, autotrophic biomass, including small algae, autotrophic flagellated protists and cyanobacteria, was associated with concentrations of dissolved N and P in the leaf litter leachates.Amendment of basal nutrients other than N and P, including micronutrients, trace elements and vitamins, increased autotrophic biomass in two leaf litter leachates (oak, Siebold's beech), suggesting that some elements other than N and P were deficient relative to the requirements of autotrophic organisms.These results indicated that the elemental composition of leaf litter leachates influences microbial community structure and heterotrophic versus autotrophic biomass in freshwater ecosystems. More importantly, the present results suggest that changes in forest vegetation surrounding freshwater ecosystems alter detritus‐based heterotrophic production relative to autotrophic production through the changes in the elemental composition (i.e. stoichiometry) of leaf litter inputs. [ABSTRACT FROM AUTHOR]

The aerobic and rod-shaped FO1 strain of iron-oxidizing bacteria was isolated from electroplating wastewater sludge using colloidal silica plates. Bacterial growth occurred at 25–30°C (optimum temperature, 27°C), pH 2.0–3.5, and in the presence of 1.0–4.0% NaCl. The X-ray diffraction analysis identified the precipitates that were formed during cell growth as jarosite. A biochemical analysis, including the assessments of the whole-cell fatty acids, quinone, and DNA G+C contents, revealed that FO1 was closely related to the genus Acidihalobacter. The 16S rRNA sequence of the FO1 gene was similar to those of the Acidihalobacter prosperus DSM 5130 (97% similarity), Ah. aeolianus DSM 14174 (100%), and Ah. yilgarnensis DSM 105917 (100%) strains. Antibiotic sensitivity tests of strain FO1 revealed that it was tolerant for gentamicin, kanamycin, and tetracycline, whereas it was sensitive to ampicillin and chloramphenicol. Moreover, strain FO1 was able to grow in a microbial electrolysis cell with continuous reduction of Fe3+ to Fe2+ on the cathode, albeit with a slight inhibition of cell growth. This study provides information regarding the genetics, bioleaching of metals, and electrochemical cultivation of halotolerant iron-oxidizing bacteria in the genus Acidihalobacter. [ABSTRACT FROM AUTHOR]

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Autotrophic bacteria are able to fix CO2 in a great diversity of habitats, even though this dissolved gas is relatively scarce at neutral pH and above. As many of these bacteria rely on CO2 fixation by ribulose 1,5-bisphospate carboxylase/oxygenase (RubisCO) for biomass generation, they must compensate for the catalytical constraints of this enzyme with CO2-concentrating mechanisms (CCMs). CCMs consist of CO2 and HCO3- transporters and carboxysomes. Carboxysomes encapsulate RubisCO and carbonic anhydrase (CA) within a protein shell and are essential for the operation of a CCM in autotrophic Bacteria that use the Calvin-Benson-Basham cycle. Members of the genus Thiomicrospira lack genes homologous to those encoding previously described CA, and prior to this work, the mechanism of function for their carboxysomes was unclear. In this paper, we provide evidence that a member of the recently discovered iota family of carbonic anhydrase enzymes (ιCA) plays a role in CO2 fixation by carboxysomes from members of Thiomicrospira and potentially other Bacteria. Carboxysome enrichments from Thiomicrospira pelophila and Thiomicrospira aerophila were found to have CA activity and contain ιCA, which is encoded in their carboxysome loci. When the gene encoding ιCA was interrupted in T. pelophila, cells could no longer grow under low-CO2 conditions, and CA activity was no longer detectable in their carboxysomes. When T. pelophila ιCA was expressed in a strain of Escherichia coli lacking native CA activity, this strain recovered an ability to grow under low CO2 conditions, and CA activity was present in crude cell extracts prepared from this strain. [ABSTRACT FROM AUTHOR]

Partial nitrification (PN) is an effective process for treating high-strength ammonium wastewater with a low COD/N (chemical oxygen demand/total nitrogen) ratio; this is because the cooperative interaction with denitrification or anammox can result in a reduction in aeration costs of approximately 25% and a reduction in the use of organic sources during biological nitrogen removal of 40%. However, the key functional microorganisms in the partial nitrification (PN) process are ammonia-oxidizing bacteria (AOB), which are autotrophic microorganisms that are influenced by carbon sources. Therefore, the COD/N ratio affects the performance of the PN process when treating high-strength ammonium wastewater. In this study, five sequence batch reactors were constructed and operated for 42 days; they were fed with synthetic high-strength ammonium wastewater (500 mg/L) with various COD/N ratios (at 0, 0.5, 1, 2, and 4). The results suggested that the PN process could be accomplished at COD/N ratios of 0 and 0.5, but its performance decreased significantly when the COD/N ratio increased to 1 due to the occurrence of simultaneous nitrification and denitrification. The AOB could not compete with the heterotrophic bacteria; as the COD/N ratios increased, the abundance of Nitrosomonas (a genus of autotrophic AOB) decreased, and it was not detected at COD/N ratios of 2 and 4. Instead, the heterotrophic nitrification and heterotrophic denitrification (HNAD) bacteria appeared, and their relative abundance increased when the COD/N ratios increased from 1 to 4. [ABSTRACT FROM AUTHOR]

Iron–carbon galvanic-cell-supported autotrophic denitrification (IC-ADN) is a burgeoning efficient and cost-effective process for low-carbon wastewater treatment. This study revealed the influence of organic carbon (OC) and dissolved oxygen (DO) on IC-ADN in terms of functional and microbiological characteristics. The nitrogen removal efficiency increased to 91.6% and 94.7% with partial organic carbon source addition to COD/TN of 1 and 3, respectively. The results of 16S rRNA high-throughput sequencing with nirS and cbbL clone libraries showed that Thiobacillus was the predominant autotrophic denitrifying bacteria (ADB) in the micro-electrolysis-based autotrophic denitrification, which obtained nitrogen removal efficiency of 80.9% after 96 h. The ADBs shifted gradually to heterotrophic denitrifying bacteria Thauera with increasing COD/TN ratio. DO concentration of 0.8 rarely affected the denitrification efficiency and the denitrifying communities. When the DO concentration increased to 2.8 mg/L, the nitrogen removal efficiency decreased to 69.1%. These results demonstrated that autotrophic denitrification was notably affected by COD/TN and high DO concentration, which could be used to acquire optimum conditions for nitrogen removal. These results provided an in-depth understanding of the influential factors for galvanic-cell-based denitrification and helped us construct a stable and highly efficient treatment process for insufficient carbon source wastewater. [ABSTRACT FROM AUTHOR]

【Objective】The paper aimed to explore the impact of different years of abandonment in tropical regions on soil carbon fixing bacterial communities in farmland, and provide theoretical basis and data support for sustainable agricultural management. 【Method】Real time quantitative PCR and high-throughput sequencing technology were used to analyze the gene abundance, community diversity, and differences of soil carbon fixing bacteria in farmland, short-term abandoned land (2＜abandoned years＜5), and long-term abandoned land (abandoned years＞5) in the central region of Hainan Island. 【Result】The abundance of cbbL gene in the soil within the region ranged from 3.11×107-2.84×108 copies/g of dry soil, showing a trend of farmland＞short-term abandoned land＞long-term abandoned land. Compared with the control farmland, long-term abandoned land reduced the Chao1 index, Observed Specifications index and Shannon index of soil carbon fixing bacteria. The dominant phyla of carbon fixing bacteria in tropical farmland soils with different abandonment years were Pseudomonadota and Actinomycetota, and the dominant genera were Bradyrhizobium, Mycobacterium, Rhodopseudomonas, Rubrivivax, Blastochlolis, Nocardia, Mesorhizobium, Dokdonella and Azospirillum, and most of them were facultative autotrophic bacteria. The overall changes in the community structure of soil carbon fixing bacteria with different abandonment years showed clustering according to each abandonment year. A total of 33 differential markers were analyzed for three different abandonment years of soil, including 17 in farmland, 5 in short-term abandonment land, and 11 in long-term abandonment land. The RDA results showed that the community structure of soil carbon fixing bacteria was significantly influenced by SOC, SWC, ROC, TP, TN, Coarse sand, pH and Fine sand. 【Conclusion】The increase in abandoned years has reduced the gene abundance of soil carbon fixing bacteria, and the community structure has also changed. Environmental factors such as SOC, SWC, ROC, TP and TN have a significant impact on the community structure of soil carbon fixing bacteria. [ABSTRACT FROM AUTHOR]

Background: Acetogens, a diverse group of anaerobic autotrophic bacteria, are promising whole-cell biocatalysts that fix CO2 during their growth. However, because of energetic constraints, acetogens exhibit slow growth and the product spectrum is often limited to acetate. Enabling acetogens to form more valuable products such as volatile fatty acids during autotrophic growth is imperative for cementing their place in the future carbon neutral industry. Co-cultivation of strains with different capabilities has the potential to ease the limiting energetic constraints. The lactate-mediated co-culture of an Acetobacterium woodii mutant strain, capable of lactate production, with the Clostridium drakei SL1 type strain can produce butyrate and hexanoate. In this study, the preceding co-culture is characterized by comparison of monocultures and different co-culture approaches. Results: C. drakei grew with H2 + CO2 as main carbon and energy source and thrived when further supplemented with D-lactate. Gas phase components and lactate were consumed in a mixotrophic manner with acetate and butyrate as main products and slight accumulation of hexanoate. Formate was periodically produced and eventually consumed by C. drakei. A lactate-mediated co-culture of the A. woodii [PbgaL_ldhD_NFP] strain, engineered for autotrophic lactate production, and C. drakei produced up to 4 ± 1.7 mM hexanoate and 18.5 ± 5.8 mM butyrate, quadrupling and doubling the respective titers compared to a non-lactate-mediated co-culture. Further co-cultivation experiments revealed the possible advantage of sequential co-culture over concurrent approaches, where both strains are inoculated simultaneously. Scanning electron microscopy of the strains revealed cell-to-cell contact between the co-culture partners. Finally, a combined pathway of A. woodii [PbgaL_ldhD_NFP] and C. drakei for chain-elongation with positive ATP yield is proposed. Conclusion: Lactate was proven to be a well-suited intermediate to combine the high gas uptake capabilities of A. woodii with the chain-elongation potential of C. drakei. The cell-to-cell contact observed here remains to be further characterized in its nature but hints towards diffusive processes being involved in the co-culture. Furthermore, the metabolic pathways involved are still speculatory for C. drakei and do not fully explain the consumption of formate while H2 + CO2 is available. This study exemplifies the potential of combining metabolically engineered and native bacterial strains in a synthetic co-culture. [ABSTRACT FROM AUTHOR]

The influence of bioturbation induced by bottom‐dwelling macrozoobenthos on nitrogen dynamics in lotic stream sediments remains unclear. In this work, we advance the understanding of faunal bioturbation in lotic environments by developing a fully‐coupled flow and multicomponent reactive transport model and investigate the influence of sediment reworking and burrow ventilation processes on nitrogenous transformations. The model results indicate that sediment reworking and burrow ventilation significantly increase nitrate (NO3−) influx, penetration depth, and reaction rates in the streambed. Denitrification rates were observed up to three times higher in beds with U‐shaped burrows compared to flatbeds. The ratio of mound height to stream water depth ratio (h/H0) is a dominant control on determining the relative importance of the sediment reworking and burrow ventilation processes in modulating nitrogenous reactions. A power‐law scaling framework is ultimately proposed to predict NO3− removal efficiency based on the Damköhler number in bioturbated lotic streambeds. Plain Language Summary: The increase in nitrate (NO3−) levels can harm rivers by causing problems like eutrophication, toxic algal blooms, and low oxygen levels. Microbes, like those involved in denitrification, can help reduce NO3− levels in the riverbed, where surface water and groundwater mix. Creatures like macroinvertebrates that live in the riverbed also play a role in how NO3− moves and is used. We wanted to know if these creatures, by disturbing the sediment and irrigating it, change how NO3− behaves in the riverbed. Our computer modeling showed that having U‐shaped burrows in the sediment can enhance the rate at which NO3− is removed, up to three times more than in flatbed sediments. As the ratio of the mound height to the total depth becomes less than 0.1, the influence of sediment reworking on NO3− influx and consumption rates decreases, and burrow ventilation becomes more important. We also came up with a way to predict NO3− removal efficiency in bioturbated riverbeds under flowing water conditions. These findings underscore the significance of bioturbation in rivers with moving water and have important implications for managing and restoring rivers. Key Points: Developing a Navier‐Stokes‐Brinkman‐Darcy‐Reaction fully‐coupled approach to study interplay between nitrogen cycling and faunal bioturbationSediment reworking and burrow ventilation processes could significantly alter the nitrogenous transformations in low flow environmentsA power‐law scaling framework can be used to predict nitrate removal efficiency within the bioturbated sediments from the Damköhler number [ABSTRACT FROM AUTHOR]

Autotrophy is the basis for complex life on Earth. Central to this process is rubisco—the enzyme that catalyzes almost all carbon fixation on the planet. Yet, with only a small fraction of rubisco diversity kinetically characterized so far, the underlying biological factors driving the evolution of fast rubiscos in nature remain unclear. We conducted a high-throughput kinetic characterization of over 100 bacterial form I rubiscos, the most ubiquitous group of rubisco sequences in nature, to uncover the determinants of rubisco's carboxylation velocity. We show that the presence of a carboxysome CO2 concentrating mechanism correlates with faster rubiscos with a median fivefold higher rate. In contrast to prior studies, we find that rubiscos originating from α-cyanobacteria exhibit the highest carboxylation rates among form I enzymes (≈10 s−1 median versus <7 s−1 in other groups). Our study systematically reveals biological and environmental properties associated with kinetic variation across rubiscos from nature. Synopsis: Form I rubisco, known for its slow kinetics in plants and algae, exhibits a great unexplored diversity in autotrophic bacteria. This article represents the first large-scale survey of bacterial form I rubisco kinetics and reveals unifying features of fast carboxylating rubiscos. Over 100 homologs were systematically screened, spanning the wide genetic diversity of form I rubisco enzymes across a variety of ecological niches and metabolic profiles. Phototrophy and carboxysome association are correlated with fast-carboxylating rubiscos. α-cyanobacteria emerges as the bacterial clade expressing the fastest form I rubiscos on Earth. Bacterial rubisco enzymes associated with carboxysomes have the fastest CO2-fixing rates. [ABSTRACT FROM AUTHOR]

In this study, CH4 production capacity of nitrification bacteria (NB) obtained from the submerged biofilter in the laboratory was investigated. Biochemical methane potential (BMP) test was carried out with the NB amount of zero (control, CR), 5% (R1), 10% (R2), and 15% (R3) at a temperature of about 37 ± 0.5°C. Compared to the CR, significantly higher cumulative CH4 volume of about 290, 490, and 715 mL were determined in the R1, R2, and R3, respectively. All the applied kinetic models gave good results (R2 ≥0.97), while the Transference Function and First-order models provided the better R2 values. The delay phase (λ) was not observed in the AD process, and CH4 production started immediately on the first day of operation. The predicted k value of 0.133 day−1 was high in CR, while it was approximately between 0.078 and 0.112 day−1 for the higher amount of NB containing BMP units, which indicated that the AD required long reaction time. [ABSTRACT FROM AUTHOR]

Oligotrophic deep-water lakes are unique and sensitive ecosystems with limited nutrient availability. Understanding bacterial communities within these lakes is crucial for assessing ecosystem health, biogeochemical cycling, and responses to environmental changes. In this study, we investigated the seasonal and vertical dynamics of both free-living (FL) and particle-attached (PA) bacteria in Lake Fuxian, a typical oligotrophic deep freshwater lake in southeast China. Our findings revealed distinct seasonal and vertical dynamics of FL and PA bacterial communities, driven by similar physiochemical environmental factors. PA bacteria exhibited higher a- and ß-diversity and were enriched with Proteobacteria, Cyanobacteria, Firmicutes, Patescibacteria, Planctomycetota, and Verrucomicrobiota, while FL bacteria were enriched with Actinobacteria and Bacteroidota. FL bacteria showed enrichment in putative functions related to chemoheterotrophy and aerobic anoxygenic photosynthesis, whereas the PA fraction was enriched with intracellular parasites (mainly contributed by Rickettsiales, Chlamydiales, and Legionellales) and nitrogen metabolism functions. Deterministic processes predominantly shaped the assembly of both FL and PA bacterial communities, with stochastic processes playing a greater role in the FL fraction. Network analysis revealed extensive species interactions, with a higher proportion of positively correlated edges in the PA network, indicating mutualistic or cooperative interactions. Cyanobium, Comamonadaceae, and Roseomonas were identified as keystone taxa in the PA network, underscoring potential cooperation between autotrophic and heterotrophic bacteria in organic particle microhabitats. Overall, the disparities in bacterial diversity, community composition, putative function, and network characteristics between FL and PA fractions highlight their adaptation to distinct ecological niches within these unique lake ecosystems. [ABSTRACT FROM AUTHOR]

Microplastic (MP) pollution likely affects global soil carbon (C) dynamics, yet it remains uncertain how and to what extent MP influences soil respiration. Here, we report on a global meta‐analysis to determine the effects of MP pollution on the soil microbiome and CO2 emission. We found that MP pollution significantly increased the contents of soil organic C (SOC) (21%) and dissolved organic C (DOC) (12%), the activity of fluorescein diacetate hydrolase (FDAse) (10%), and microbial biomass (17%), but led to a decrease in microbial diversity (3%). In particular, increases in soil C components and microbial biomass further promote CO2 emission (25%) from soil, but with a much higher effect of MPs on these emissions than on soil C components and microbial biomass. The effect could be attributed to the opposite effects of MPs on microbial biomass vs. diversity, as soil MP accumulation recruited some functionally important bacteria and provided additional C substrates for specific heterotrophic microorganisms, while inhibiting the growth of autotrophic taxa (e.g., Chloroflexi, Cyanobacteria). This study reveals that MP pollution can increase soil CO2 emission by causing shifts in the soil microbiome. These results underscore the potential importance of plastic pollution for terrestrial C fluxes, and thus climate feedbacks. [ABSTRACT FROM AUTHOR]

It has been previously shown that devices based on microbial biofilms can generate hydrovoltaic energy from water evaporation. However, the potential of hydrovoltaic energy as an energy source for microbial growth has remained unexplored. Here, we show that the electroautotrophic bacterium Rhodopseudomonas palustris can directly utilize evaporation-induced hydrovoltaic electrons for growth within biofilms through extracellular electron uptake, with a strong reliance on carbon fixation coupled with nitrate reduction. We obtained similar results with two other electroautotrophic bacterial species. Although the energy conversion efficiency for microbial growth based on hydrovoltaic energy is low compared to other processes such as photosynthesis, we hypothesize that hydrovoltaic energy may potentially contribute to microbial survival and growth in energy-limited environments, given the ubiquity of microbial biofilms and water evaporation conditions. Devices based on microbial biofilms can be used to generate hydrovoltaic energy from water evaporation. Here, Ren et al. show that, in addition, electroautotrophic bacteria can use evaporation-induced hydrovoltaic electrons for growth in biofilms. [ABSTRACT FROM AUTHOR]

The effects of resource subsidies on a recipient ecosystem depends on a variety of factors. Firstly, increasing the supply of limiting nutrients tends to increase the accumulation of biomass across different compartments of the recipient food web. Secondly, in the case of aquatic microorganisms, this accumulation may also be contingent on inputs of energy through light, mediating interactions between heterotrophic bacteria and autotrophic algae. Thirdly, macroscopic consumers feed upon microorganisms and recycle nutrients through excretion and egestion, profoundly affecting nutrient cycling.In order to examine the context‐dependency of nutrient cycling in aquatic systems, we performed an experiment in mesocosms where we followed the responses of dissolved nutrients, microorganisms, and larvae of the cosmopolitan mosquito Culex quinquefasciatus (Diptera: Culicidae) to two terrestrial subsidies differing in carbon (C):nutrient, in combination with two light intensities.We found that the interactions amongst bacteria and algae themselves remained generally unimportant after accounting for treatment effects, and that light did mediate some of the effects of nutrient subsidies on microorganisms. We also found that the presence of mosquito larvae was associated with altered concentrations of nitrogen (N) in some treatments, ultimately benefitting algae. Finally, we found that low C:nutrient subsidies generally increased the development rate of mosquito larvae, and that increased light exposure led to higher mosquito survival.Overall, these patterns may be explained by strong nitrogen limitation in our system, causing both group of microorganisms to respond similarly to variations in nutrient supply without direct covariation, and to the key role of N recycling by mosquito larvae in sustaining algal densities in exposed treatments.The context‐dependency in our study may reflect elemental or molecular constraints other than phosphorus. Our experiment thus calls for greater synthesis amongst ecological theories. [ABSTRACT FROM AUTHOR]

Non-fermentative nitrite reduction to ammonium, resulting in the release of ammonium in the environment, can be performed by a variety of enzymes found among bacteria and archaea. NrfA-dependent ammonifiers are phylogenetically diverse and are present in terrestrial and aquatic environments, and for the latter especially in sediments. NrfA-dependent ammonifiers often carry genes involved in denitrification and redox reactions with sulfur or iron compounds, suggesting that they play a role in multiple biogeochemical cycles. In most aquatic and terrestrial environments, denitrifiers dominate over nitrate ammonifiers, and denitrification is the dominating process of nitrate reduction. However, nitrate ammonification rates can be significant under certain redox conditions. Nitrate ammonifiers are a taxonomically diverse group of microorganisms that reduce nitrate to ammonium, which is released, and thereby contribute to the retention of nitrogen in ecosystems. Despite their importance for understanding the fate of nitrate, they remain a largely overlooked group in the nitrogen cycle. Here, we present the latest advances on free-living microorganisms using NrfA to reduce nitrite during ammonification. We describe their diversity and ecology in terrestrial and aquatic environments, as well as the environmental factors influencing the competition for nitrate with denitrifiers that reduce nitrate to gaseous nitrogen species, including the greenhouse gas nitrous oxide (N 2 O). We further review the capacity of ammonifiers for other redox reactions, showing that they likely play multiple roles in the cycling of elements. [ABSTRACT FROM AUTHOR]

Carboxysomes, responsible for a substantial fraction of CO2 fixation on Earth, are proteinaceous microcompartments found in many autotrophic members of domain Bacteria, primarily from the phyla Proteobacteria and Cyanobacteria. Carboxysomes facilitate CO2 fixation by the Calvin-Benson-Bassham (CBB) cycle, particularly under conditions where the CO2 concentration is variable or low, or O2 is abundant. These microcompartments are composed of an icosahedral shell containing the enzymes ribulose 1,5-carboxylase/oxygenase (RubisCO) and carbonic anhydrase. They function as part of a CO2 concentrating mechanism, in which cells accumulate HCO3 - in the cytoplasm via active transport, HCO3 - enters the carboxysomes through pores in the carboxysomal shell proteins, and carboxysomal carbonic anhydrase facilitates the conversion of HCO3 - to CO2, which RubisCO fixes. Two forms of carboxysomes have been described: a-carboxysomes and ß-carboxysomes, which arose independently from ancestral microcompartments. The a-carboxysomes present in Proteobacteria and some Cyanobacteria have shells comprised of four types of proteins [CsoS1 hexamers, CsoS4 pentamers, CsoS2 assembly proteins, and a-carboxysomal carbonic anhydrase (CsoSCA)], and contain form IA RubisCO (CbbL and CbbS). In the majority of cases, these components are encoded in the genome near each other in a gene locus, and transcribed together as an operon. Interestingly, genome sequencing has revealed some a-carboxysome loci that are missing genes encoding one or more of these components. Some loci lack the genes encoding RubisCO, others lack a gene encoding carbonic anhydrase, some loci are missing shell protein genes, and in some organisms, genes homologous to those encoding the carboxysome-associated carbonic anhydrase are the only carboxysomerelated genes present in the genome. Given that RubisCO, assembly factors, carbonic anhydrase, and shell proteins are all essential for carboxysome function, these absences are quite intriguing. In this review, we provide an overview of the most recent studies of the structural components of carboxysomes, describe the genomic context and taxonomic distribution of atypical carboxysome loci, and propose functions for these variants. We suggest that these atypical loci are JEEPs, which have modified functions based on the presence of Just Enough Essential Parts. [ABSTRACT FROM AUTHOR]

The hypersensitivity of anammox bacteria toward fluctuating temperature (seasonal) conditions significantly limits its real-world application. Biomass immobilization alleviates the impact of environmental shocks on the anammox process. In this study (291 d), a sequencing batch reactor engaging dishwashing scrubbers as model waste biocarriers and an amalgamation of activated, anaerobic, and anammox sludge (1:1:0.5 ratio) as inoculum (at influent pH 8.0) were deployed for the startup of the anammox process. Intriguingly, the SBR was run at ambient temperature (6–37 °C) at varying nitrogen loading rates (g N m−3 d−1) of 20, 30, 40, 46.4, 58, 60, 81.2, 92.8, and 116. Notably, anammox activation took place at ⁓247 d wherein the reactor performance improved and exhibited stable nitrogen removal (NH4+–N, NO2−–N and total nitrogen removals were 100, 99, and 72.04%, respectively). Additionally, post 279 days of reactor operation (280 – 291 d), the reactor demonstrated an average total nitrogen removal rate (g N m−3 d−1) of 88.2 at a maximum nitrogen loading rate (g N m−3 d−1) of 116. The 16S rRNA gene sequencing results revealed that Anammox bacteria predominated in the reactor, highlighting the fact that the reported increase in the percentage abundance of Candidatus Kuenenia at 266 d was exorbitantly higher (41.69%) than inoculum sludge (0.18%). Nitrospira (23.9%) and Nitrosomonas (4.32%), in addition to anammox, were found in high concentrations, suggesting presence of dissolved oxygen in the system. [ABSTRACT FROM AUTHOR]

Aha Lake artificial reservoir wetland, Niangniang Mountain karst mountain wetland, and Caohai plateau lake wetland are typical karst wetlands in Guizhou Province with unique topography and geomorphic features. They were selected as research objects in this study to explore microorganisms and functional genes in nitrogen metabolism adopting macro-genome sequencing technology. It was found that Proteobacteria, Actinobacteria, and Acidobacteria were the dominant phyla in nitrogen metabolism in these three wetlands, similar to previous studies. However, at the genus level, there was a significant difference, with the dominant bacteria being Bradyrhizobium, Methylocystis, and Anaeromyxobacter. Six nitrogen metabolism pathways, including nitrogen fixation, nitrification, denitrification, dissimilatory nitrate reduction, assimilatory nitrate reduction, and complete nitrification, comammox, were revealed, but anaerobic ammonia oxidation genes were not detected. Nitrogen metabolism microorganisms and pathways were more affected by SOM, pH, NO3−, and EC in karst wetlands. This study further discussed microorganisms and functions of nitrogen metabolism in karst wetlands, which was of great significance to nitrogen cycles of karst wetland ecosystems. [ABSTRACT FROM AUTHOR]

Tetrathionate hydrolase (TTH) is a unique enzyme found in acidophilic sulfur-oxidizing microorganisms, such as bacteria and archaea. This enzyme catalyzes the hydrolysis of tetrathionate to thiosulfate, elemental sulfur, and sulfate. It is also involved in dissimilatory sulfur oxidation metabolism, the S4-intermediate pathway. TTHs have been purified and characterized from acidophilic autotrophic sulfur-oxidizing microorganisms. All purified TTHs show an optimum pH in the acidic range, suggesting that they are localized in the periplasmic space or outer membrane. In particular, the gene encoding TTH from Acidithiobacillus ferrooxidans (Af-tth) was identified and recombinantly expressed in Escherichia coli cells. TTH activity could be recovered from the recombinant inclusion bodies by acid refolding treatment for crystallization. The mechanism of tetrathionate hydrolysis was then elucidated by X-ray crystal structure analysis. Af-tth is highly expressed in tetrathionate-grown cells but not in iron-grown cells. These unique structural properties, reaction mechanisms, gene expression, and regulatory mechanisms are discussed in this review. [ABSTRACT FROM AUTHOR]

Using dissolved inorganic carbon (DIC) as a major carbon source, as autotrophs do, is complicated by the bedeviling nature of this substance. Autotrophs using the Calvin-Benson-Bassham cycle (CBB) are known to make use of a toolkit comprised of DIC transporters and carbonic anhydrase enzymes (CA) to facilitate DIC fixation. This minireview provides a brief overview of the current understanding of how toolkit function facilitates DIC fixation in Cyanobacteria and some Proteobacteria using the CBB and continues with a survey of the DIC toolkit gene presence in organisms using different versions of the CBB and other autotrophic pathways (reductive citric acid cycle, Wood-Ljungdahl pathway, hydroxypropionate bicycle, hydroxypropionate-hydroxybutyrate cycle, and dicarboxylate-hydroxybutyrate cycle). The potential function of toolkit gene products in these organisms is discussed in terms of CO2 and HCO3 - supply from the environment and demand by the autotrophic pathway. The presence of DIC toolkit genes in autotrophic organisms beyond those using the CBB suggests the relevance of DIC metabolism to these organisms and provides a basis for better engineering of these organisms for industrial and agricultural purposes. [ABSTRACT FROM AUTHOR]

Induced partial saturation (IPS) is a new foundation treatment method for mitigating soil liquefaction using biogas. A series of laboratory tests were performed to demonstrate the influencing factors of IPS using Pseudomonas stutzeri biogas. On the basis of the optimal biogas production conditions, the intervention effect of Pseudomonas stutzeri biogas on the foundation deformation under buildings was investigated based on shaking table tests. The test results showed that the best carbon source in the denitrification process of Pseudomonas stutzeri biogas is sodium citrate. The most effective initial value of optical density-based concentration was 0.1. The carbon–nitrogen ratio (C/N) of the bacterium suspension was used as the index to control the saturation. The degree of saturation reduction showed a good linear correlation with the C/N. The optimum temperature of this method was between 20 °C and 30 °C. The most suitable pH value was between 7 and 9. The environmental factors had minimal influence on the degree of saturation reduction but had a significant effect on the average rate of gas generation and the period of initial stagnation. After Pseudomonas stutzeri biogas desaturation, the settlement of the building was greatly reduced. The settlement of saturation of 92.5% sand foundation reached 17.1 mm, and the 85% saturation was only 10.6 mm. These results provide a good foundation for the feasibility of utilizing Pseudomonas stutzeri biogas mitigation of the liquefaction hazard of sand. [ABSTRACT FROM AUTHOR]

The increased concentration of CO2 in the atmosphere has a strong impact on global warming. Therefore, efficient technologies must be used to reduce CO2 emissions. One of the methods is the biofixation of CO2 by microalgae and cyanobacteria. This is now a widely described technology that can improve the economics of biomass production and reduce CO2 emissions. There are no reports on the possibility of using it to clean exhaust gases from biogas combustion. The aim of the research was to determine the possibility of using Arthrospira platensis cultures to remove CO2 from biogas combustion. The efficiency of biomass production and the effectiveness of biological CO2 fixation were evaluated. The use of exhaust gases led to a more efficient increase in cyanobacterial biomass. The growth rate in the exponential phase was 209 ± 17 mgVS/L·day, allowing a biomass concentration of 2040 ± 49 mgVS/L. However, the use of exhaust gases led to a decrease in the pH of the culture medium and a rapid decline in the Arthrospira platensis population. The cyanobacteria effectively fixed CO2, and its concentration was limited from 13 ± 1% to 1.3 ± 0.7%. There was no influence of the exhaust gases on changes in the qualitative composition of the cyanobacterial biomass. In the culture fed with exhaust gas, the A. platensis population quickly entered the death phase, which requires close monitoring. This is an important indication for potential operators of large-scale photobioreactors. [ABSTRACT FROM AUTHOR]

The biological denitrification of low-C/N wastewater is a great challenge in treatment plants due to the lack of microorganisms with heterotrophic nitrification–aerobic denitrification (HN-AD) abilities. In this study, Bacillus sp. L2 was isolated from aeration tank water samples using a nitrification medium and screened for its ability to perform HN-AD in low-C/N wastewater. The strain showed a maximum NH4+-N removal rate of 98.37% under low-C/N conditions. In the presence of a mixed N source, strain L2 was capable of completely removing NH4+-N within 24 h. Furthermore, optimal nitrogen removal conditions for strain L2 were found to be C/N = 9, pH = 9, and sodium acetate as the C source. Under optimal conditions, the strain was able to maintain a high NH4+-N removal rate under 0–3% salinity and an NH4+-N concentration of 200 mg/L or less. The denitrification pathways of strain L2 were NH4+→NH2OH→NO2−(↔NO3−)→NO→N2O→N2 and NH4+→NH2OH→NO→N2O→N2. Furthermore, semi-continuous wastewater treatment was conducted using immobilized technology, which resulted in more than 82% NH4+-N removal after three cycles of reuse. This study demonstrates the great potential of Bacillus sp. L2 in wastewater treatment applications. [ABSTRACT FROM AUTHOR]

Cyanobacteria are excellent autotrophic photosynthetic chassis employed in synthetic biology, and previous studies have suggested that they have alkaline tolerance but low acid tolerance, significantly limiting their productivity as photosynthetic chassis and necessitating investigations into the acid stress resistance mechanism. In this study, differentially expressed genes were obtained by RNA sequencing-based comparative transcriptomic analysis under long-term acidic stress conditions and acidic shock treatment, in the model cyanobacterium Synechococcus elongatus PCC 7942. A pathway enrichment analysis revealed the upregulated and downregulated pathways during long-term acidic and shock stress treatment. The subsequent single gene knockout and phenotype analysis showed that under acidic stress conditions, the strains with chlL, chlN, pex, synpcc7942_2038, synpcc7942_1890, or synpcc7942_2547 knocked out grew worse than the wild type, suggesting their involvement in acid tolerance. This finding was further confirmed by introducing the corresponding genes back into the knockout mutant individually. Moreover, individual overexpression of the chlL and chlN genes in the wild type successfully improved the tolerance of S. elongatus PCC 7942 to acidic stress. This work successfully identified six genes involved in acidic stress responses, and overexpressing chIL or chIN individually successfully improved acid tolerance in S. elongatus PCC 7942, providing valuable information to better understand the acid resistance mechanism in S. elongatus PCC 7942 and novel insights into the robustness and tolerance engineering of cyanobacterial chassis. Key points: • DEGs were identified by RNA-seq based transcriptomics analysis in response to acidic stress in S. elongatus PCC 7942. • Six genes were identified to be involved in acid tolerance in S. elongatus PCC 7942. • Overexpression of chIL or chIN individually successfully improved the acid tolerance of S. elongatus PCC 7942. [ABSTRACT FROM AUTHOR]

Introduction: Autotrophic bacteria play an important role in carbon dioxide fixation and are widespread in terrestrial ecosystems. However, the biogeographic patterns of autotrophic bacteria and the driving factors still remain poorly understood. Methods: Herein, we conducted a 391-km north to south transect (mean annual precipitation <600 mm) survey in the Loess Plateau of China, to investigate the biogeographic distributions of autotrophic bacteria (RubisCO cbbL and cbbM genes) and the environmental drivers across different latitude sites with clear vegetational and climatic gradients. Results and discussion: The soils in northern region with lower precipitation are dominated by grassland/forest, which is typically separated from the soils in southern region with higher precipitation. The community structure of autotrophic bacterial cbbL and cbbM genes generally differed between the soils in the southern and northern Loess Plateau, suggesting that precipitation and its related land use practices/ecosystem types, rather than local soil properties, are more important in shaping the soil autotrophic microorganisms. The cbbLcontaining generalist OTUs were almost equally abundant across the northern and southern Loess Plateau, while the cbbM-containing bacterial taxa were more prevalent in the low precipitation northern region. Such differences indicate differentiate distribution patterns of cbbM- and cbbL-containing bacteria across the north to south transect. Our results suggest that the community composition and the differentiate distributions of soil cbbL- and cbbM-containing bacterial communities depend on precipitation and the related ecosystem types in the north to south transect in the Loess Plateau of China. [ABSTRACT FROM AUTHOR]

Microbial pigments play a significant role in glacier albedo reduction, thereby contributing to accelerated glacier retreat. The Tibetan Plateau has experienced rapid glacier retreat in recent decades due to global warming, yet there is limited understanding of microbial pigment distribution in the region. Here, we investigated the pigment concentration and composition in cryoconite from four glaciers. Our results showed that chlorophylls were the dominant pigments in Palong No. 4 (PL) and Jiemayangzong (JMYZ) glaciers located in the south of the Tibetan Plateau, while carotenoids were dominant in Qiangyong (QY) and Tanggula (TGL) glaciers located in the central region. Additionally, the chlorophyll b to chlorophyll a ratio, which is an indicator of the algae‐to‐cyanobacteria ratio, was higher in PL and JMYZ compared to QY and TGL. By using Random Forest Regression and Structural Equation Modelling, we determined that the concentrations of chlorophyll a, chlorophyll b, and carotenoids were associated with autotrophic bacteria relative abundance, climatic factors, and a combination of bacterial and climatic factors, respectively. This study is the first to describe the distribution of microbial pigments in cryoconite from Tibetan glaciers, providing additional support on the influence of algal pigment on glacier retreat. [ABSTRACT FROM AUTHOR]

In the field of wastewater treatment, nitrate nitrogen (NO3−-N) is one of the significant contaminants of concern. Sulfur autotrophic denitrification technology, which uses a variety of sulfur-based electron donors to reduce NO3−-N to nitrogen (N2) through sulfur autotrophic denitrification bacteria, has emerged as a novel nitrogen removal technology to replace heterotrophic denitrification in the field of wastewater treatment due to its low cost, environmental friendliness, and high nitrogen removal efficiency. This paper reviews the advance of reduced sulfur compounds (such as elemental sulfur, sulfide, and thiosulfate) and iron sulfides (such as ferrous sulfide, pyrrhotite, and pyrite) electron donors for treating NO3−-N in wastewater by sulfur autotrophic denitrification technology, including the dominant bacteria types and the sulfur autotrophic denitrification process based on various electron donors are introduced in detail, and their operating costs, nitrogen removal performance and impacts on the ecological environment are analyzed and compared. Moreover, the engineering applications of sulfur-based electron donor autotrophic denitrification technology were comprehensively summarized. According to the literature review, the focus of future industry research were discussed from several aspects as well, which would provide ideas for the application and optimization of the sulfur autotrophic denitrification process for deep and efficient removal of NO3−-N in wastewater. [ABSTRACT FROM AUTHOR]

As the problem of eutrophication of water bodies and nitrate pollution of surface and groundwater is becoming more and more prominent, deep denitrification of wastewater can effectively reduce the amount of nitrate nitrogen (NO3−-N) discharged into natural water bodies. To solve this problem, in this research, the autotrophic denitrifying bacteria were incorporated in an autotrophic denitrification simulator equipped with magnetic pyrite to remove NO3−-N and total nitrogen (TN) from wastewater. The purified strains were inoculated into municipal sewage. When the ratio of magnetic pyrite to quartz sand was 1:1 and the particle size of the filler was 0.5–1 mm, the removal rate of NO3−-N and TN was optimized, at 93.52% and 83.22%, respectively. Sulphate (SO42−) concentrations will level off during stable system operation, and SO42− concentrations show a positive correlation with NO3−-N and TN removal. The 16s rDNA sequencing analysis of the screened sludge showed that the main phyla in the screened and purified sludge were Epsilonbacteraeota and Proteobacteria, with an abundance of 65.83% and 26.88%, and the final enriched products were dominated by Sulfurimonas and Thiobacillus, with an abundance of 64.91% and 9.32%, respectively. The results showed that autotrophic denitrifying bacteria could be screened and purified using thiosulfate as a substrate, and that the use of magneto pyrite as an electron donor reduced most of the NO3−-N to N2, while reducing the TN content. [ABSTRACT FROM AUTHOR]

We show that epilithic biofilms are a relevant nitrogen (N) source in a rocky mountain range in Brazil. During different seasons, we quantified nitrate, ammonium, dissolved organic N (DON) and total dissolved N (TDN) leached by a simulated short rain event. We quantified the epilithic autotrophic biomass by taxonomic groups and its correlation with leached N. We hypothesized that leached N would be correlated to heterocystous cyanobacteria biomass since they are more efficient N2 fixers. We estimated a landscape N supply of 8.5 kg.ha−1.year−1 considering the mean precipitation in the region. TDN in leachate was mainly composed of DON (83.8% ± 22%), followed by nitrate (12.1% ± 3%) and ammonium (5% ± 5%). The autotrophic epilithic community was mainly composed of non‐heterocystous (Gloeocapsopsis) and heterocystous cyanobacteria (Scytonema and Stigonema), except for a site more commonly affected by fire events that showed a dominance of Chlorophyta. Biogeochemical upscaling was facilitated by the fact that N leaching was not different among sites or related to autotrophic epilithic biomass or assemblage composition. In conclusion, the capacity of epilithic biofilms to provide N to surrounding systems is an ecosystem service that underscores the necessity to conserve them and their habitats. [ABSTRACT FROM AUTHOR]

Aquaculture is prone to pH fluctuations depending on dominating microbial pathway in the management. The present study takes advantage of the influence of pH in changing the properties of charcoal to condition the pH and improve nutrient removal. Two Synthetic aquaculture wastewaters of 100 mg/L TAN were designed to test the pathway's nutrient removal and pH stability. Glucose at 15 C/N was added to one wastewater, favoring heterotrophic pathway. The other was free of organic carbon, favoring autotrophic pathway. Powdered charcoal was added to each pathway at 0.5, 1.0, 2.0, and 4.0% (charcoal weight/volume of media) compared to the 0 % group without charcoal. The result revealed that as charcoal percentages increase, the pH shifts towards stabilization and improves nutrient removal (p = 0.05). At 4.0% charcoal, the pH was stabilized at 6.0 - 7.5 in heterotrophic and 7.5 - 7.9 in autotrophic pathways, which are within the optimum range for the survival of aquatic organisms, corresponding to the removal efficiency of TAN (99.96 and 50 %), and phosphate (55 and 17 %) within 6 days. Hence, for every 100 mg/L of TAN in wastewater, 4.0% of the wastewater volume as charcoal could stabilize pH and improve microbial nutrient removal. [ABSTRACT FROM AUTHOR]

Background: Heterotrophic microbes inhabiting the dark ocean largely depend on the settling of organic matter from the sunlit ocean. However, this sinking of organic materials is insufficient to cover their demand for energy and alternative sources such as chemoautotrophy have been proposed. Reduced sulfur compounds, such as thiosulfate, are a potential energy source for both auto- and heterotrophic marine prokaryotes. Methods: Seawater samples were collected from Labrador Sea Water (LSW, ~ 2000 m depth) in the North Atlantic and incubated in the dark at in situ temperature unamended, amended with 1 µM thiosulfate, or with 1 µM thiosulfate plus 10 µM glucose and 10 µM acetate (thiosulfate plus dissolved organic matter, DOM). Inorganic carbon fixation was measured in the different treatments and samples for metatranscriptomic analyses were collected after 1 h and 72 h of incubation. Results: Amendment of LSW with thiosulfate and thiosulfate plus DOM enhanced prokaryotic inorganic carbon fixation. The energy generated via chemoautotrophy and heterotrophy in the amended prokaryotic communities was used for the biosynthesis of glycogen and phospholipids as storage molecules. The addition of thiosulfate stimulated unclassified bacteria, sulfur-oxidizing Deltaproteobacteria (SAR324 cluster bacteria), Epsilonproteobacteria (Sulfurimonas sp.), and Gammaproteobacteria (SUP05 cluster bacteria), whereas, the amendment with thiosulfate plus DOM stimulated typically copiotrophic Gammaproteobacteria (closely related to Vibrio sp. and Pseudoalteromonas sp.). Conclusions: The gene expression pattern of thiosulfate utilizing microbes specifically of genes involved in energy production via sulfur oxidation and coupled to CO2 fixation pathways coincided with the change in the transcriptional profile of the heterotrophic prokaryotic community (genes involved in promoting energy storage), suggesting a fine-tuned metabolic interplay between chemoautotrophic and heterotrophic microbes in the dark ocean. 13R5usaxM1iwstSWbHDM6j Video Abstract [ABSTRACT FROM AUTHOR]

The Moon‐forming impact vaporized part of Earth's mantle, and turned the rest into a magma ocean, from which carbon dioxide degassed into the atmosphere, where it stayed until water rained out to form the oceans. The rain dissolved CO2 and made it available to react with transition metal catalysts in the Earth's crust so as to ultimately generate the organic compounds that form the backbone of microbial metabolism. The Moon‐forming impact was key in building a planet with the capacity to generate life in that it converted carbon on Earth into a homogeneous and accessible substrate for organic synthesis. Today all ecosystems, without exception, depend upon primary producers, organisms that fix CO2. According to theories of autotrophic origin, it has always been that way, because autotrophic theories posit that the first forms of life generated all the molecules needed to build a cell from CO2, forging a direct line of continuity between Earth's initial CO2‐rich atmosphere and the first microorganisms. By modern accounts these were chemolithoautotrophic archaea and bacteria that initially colonized the crust and still inhabit that environment today. [ABSTRACT FROM AUTHOR]

Mixotrophic flagellates, which have diverse nutritional modes and play important roles in connecting the microbial loop with the classical food chain, are ideal models to study the mechanisms of adaptation between different nutritional modes in protists. In their natural ecosystems, mixotrophic flagellates may encounter microalgal prey of different digestibility, which may affect the carbon flow. To date, a molecular biological view of the metabolic processes in the mixotrophic flagellate Poterioochromonas malhamensis during nutritional adaptation and feeding on microalgal prey of different digestibility is still lacking. Accordingly, this study focused on the gene expression differences in P. malhamensis under autotrophy, being fed by the digestible microalga Chlorella sorokiniana GT-1, and being fed by the indigestible microalga C. sorokiniana CMBB-146. Results showed that the growth rate of P. malhamensis under autotrophy was much lower than that when fed by digestible microalgae. Addition of C. sorokiniana CMBB-146 could only increase the growth rate of P. malhamensis in the first 3 days, but the cell concentration of P. malhamensis started to decrease gradually after 4 days. Compared to autotrophic P. malhamensis, total 6,583 and 3,510 genes were significantly and differentially expressed in P. malhamensis fed by digestible microalgae and indigestible microalgae, respectively. Compared to autotrophic cells, genes related to the ribosome, lysosome, glycolysis, gluconeogenesis, TCA cycle, ß-oxidation, duplication, and ß-1,3-glucan in P. malhamensis grazing on digestible prey were up-regulated, while genes related to light harvesting and key enzymes referring to chlorophyll were down-regulated. Genes related to apoptosis and necrosis in P. malhamensis were up-regulated after grazing on indigestible microalgae compared to the autotrophic group, which we suggest is associated with the up-regulation of genes related to lysosome enzymes. This study provides abundant information on the potential intracellular physiological responses of P. malhamensis during the process of nutritional adaptation. [ABSTRACT FROM AUTHOR]

Across bacteria, protein-based organelles called bacterial microcompartments (BMCs) encapsulate key enzymes to regulate their activities. The model BMC is the carboxysome that encapsulates enzymes for CO2 fixation to increase efficiency and is found in many autotrophic bacteria, such as cyanobacteria. Despite their importance in the global carbon cycle, little is known about how carboxysomes are spatially regulated. We recently identified the two-factor system required for the maintenance of carboxysome distribution (McdAB). McdA drives the equal spacing of carboxysomes via interactions with McdB, which associates with carboxysomes. McdA is a ParA/MinD ATPase, a protein family well studied in positioning diverse cellular structures in bacteria. However, the adaptor proteins like McdB that connect these ATPases to their cargos are extremely diverse. In fact, McdB represents a completely unstudied class of proteins. Despite the diversity, many adaptor proteins undergo phase separation, but functional roles remain unclear. Here, we define the domain architecture of McdB from the model cyanobacterium Synechococcus elongatus PCC 7942, and dissect its mode of biomolecular condensate formation. We identify an N-terminal intrinsically disordered region (IDR) that modulates condensate solubility, a central coiled-coil dimerizing domain that drives condensate formation, and a C-terminal domain that trimerizes McdB dimers and provides increased valency for condensate formation. We then identify critical basic residues in the IDR, which we mutate to glutamines to solubilize condensates. Finally, we find that a condensate-defective mutant of McdB has altered association with carboxysomes and influences carboxysome enzyme content. The results have broad implications for understanding spatial organization of BMCs and the molecular grammar of protein condensates. [ABSTRACT FROM AUTHOR]

IntroductionAutotrophic bacteria play an important role in carbon dioxide fixation and are widespread in terrestrial ecosystems. However, the biogeographic patterns of autotrophic bacteria and the driving factors still remain poorly understood.MethodsHerein, we conducted a 391-km north to south transect (mean annual precipitation

Despite their non-negligible representation among the airborne bioparticles and known allergenicity, autotrophic microorganisms—microalgae and cyanobacteria—are not commonly reported or studied by aerobiological monitoring stations due to the challenging identification in their desiccated and fragmented state. Using a gravimetric method with open plates at the same time as Hirst-type volumetric bioparticle sampler, we were able to cultivate the autotrophic microorganisms and use it as a reference for correct retrospective identification of the microalgae and cyanobacteria captured by the volumetric trap. Only in this way, reliable data on their presence in the air of a given area can be obtained and analysed with regard to their temporal variation and environmental factors. We gained these data for an inland temperate region over 3 years (2018, 2020–2021), identifying the microalgal genera Bracteacoccus, Desmococcus, Geminella, Chlorella, Klebsormidium, and Stichococcus (Chlorophyta) and cyanobacterium Nostoc in the volumetric trap samples and three more in the cultivated samples. The mean annual concentration recorded over 3 years was 19,182 cells*day/m3, with the greatest contribution from the genus Bracteacoccus (57%). Unlike some other bioparticles like pollen grains, autotrophic microorganisms were present in the samples over the course of the whole year, with greatest abundance in February and April. The peak daily concentration reached the highest value (1011 cells/m3) in 2021, while the mean daily concentration during the three analysed years was 56 cells/m3. The analysis of intra-diurnal patterns showed their increased presence in daylight hours, with a peak between 2 and 4 p.m. for most genera, which is especially important due to their potential to trigger allergy symptoms. From the environmental factors, wind speed had a most significant positive association with their concentration, while relative air humidity had a negative influence. [ABSTRACT FROM AUTHOR]

Metabolite-level regulation of enzyme activity is important for microbes to cope with environmental shifts. Knowledge of such regulations can also guide strain engineering for biotechnology. Here we apply limited proteolysis-small molecule mapping (LiP-SMap) to identify and compare metabolite-protein interactions in the proteomes of two cyanobacteria and two lithoautotrophic bacteria that fix CO2 using the Calvin cycle. Clustering analysis of the hundreds of detected interactions shows that some metabolites interact in a species-specific manner. We estimate that approximately 35% of interacting metabolites affect enzyme activity in vitro, and the effect is often minor. Using LiP-SMap data as a guide, we find that the Calvin cycle intermediate glyceraldehyde-3-phosphate enhances activity of fructose-1,6/sedoheptulose-1,7-bisphosphatase (F/SBPase) from Synechocystis sp. PCC 6803 and Cupriavidus necator in reducing conditions, suggesting a convergent feed-forward activation of the cycle. In oxidizing conditions, glyceraldehyde-3-phosphate inhibits Synechocystis F/SBPase by promoting enzyme aggregation. In contrast, the glycolytic intermediate glucose-6-phosphate activates F/SBPase from Cupriavidus necator but not F/SBPase from Synechocystis. Thus, metabolite-level regulation of the Calvin cycle is more prevalent than previously appreciated. A proteolysis-coupled mass spectrometry analysis is used to examine metabolite-protein interaction in cyanobacteria and finds that the regulation exerted by metabolites on the Calvin cycle is more numerous than previously thought. [ABSTRACT FROM AUTHOR]

Extreme acidophiles thrive in harsh environments characterized by acidic pH, high concentrations of dissolved metals and high osmolarity. Most of these microorganisms are chemolithoautotrophs that obtain energy from low redox potential sources, such as the oxidation of ferrous ions. Under these conditions, the mechanisms that maintain homeostasis of proteins (proteostasis), as the main organic components of the cells, are of utmost importance. Thus, the analysis of protein chaperones is critical for understanding how these organisms deal with proteostasis under such environmental conditions. In this work, using a bioinformatics approach, we performed a comparative genomic analysis of the genes encoding classical, periplasmic and stress chaperones, and the protease systems. The analysis included 35 genomes from iron- or sulfur-oxidizing autotrophic, heterotrophic, and mixotrophic acidophilic bacteria. The results showed that classical ATP-dependent chaperones, mostly folding chaperones, are widely distributed, although they are sub-represented in some groups. Acidophilic bacteria showed redundancy of genes coding for the ATP-independent holdase chaperones RidA and Hsp20. In addition, a systematically high redundancy of genes encoding periplasmic chaperones like HtrA and YidC was also detected. In the same way, the proteolytic ATPase complexes ClpPX and Lon presented redundancy and broad distribution. The presence of genes that encoded protein variants was noticeable. In addition, genes for chaperones and protease systems were clustered within the genomes, suggesting common regulation of these activities. Finally, some genes were differentially distributed between bacteria as a function of the autotrophic or heterotrophic character of their metabolism. These results suggest that acidophiles possess an abundant and flexible proteostasis network that protects proteins in organisms living in energy-limiting and extreme environmental conditions. Therefore, our results provide a means for understanding the diversity and significance of proteostasis mechanisms in extreme acidophilic bacteria. [ABSTRACT FROM AUTHOR]

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The toxic element arsenic (As) has become the major focus of global research owing to its harmful effects on human health, resulting in the establishment of several guidelines to prevent As contamination. The widespread industrial use of As has led to its accumulation in the environment, increasing the necessity to develop effective remediation technologies. Among various treatments, such as chemical, physical, and biological treatments, used to remediate As-contaminated environments, biological methods are the most economical and eco-friendly. Microbial oxidation of arsenite (As(III)) to arsenate (As(V)) is a primary detoxification strategy for As remediation as it reduces As toxicity and alters its mobility in the environment. Here, we evaluated the self-detoxification potential of microcosms isolated from Nakdong River water by investigating the autotrophic and heterotrophic oxidation of As(III) to As(V). Experimental data revealed that As(III) was oxidized to As(V) during the autotrophic and heterotrophic growth of river water microcosms. However, the rate of oxidation was significantly higher under heterotrophic conditions because of the higher cell growth and density in an organic-matter-rich environment compared to that under autotrophic conditions without the addition of external organic matter. At an As(III) concentration > 5 mM, autotrophic As(III) oxidation remained incomplete, even after an extended incubation time. This inhibition can be attributed to the toxic effect of the high contaminant concentration on bacterial growth and the acidification of the growth medium with the oxidation of As(III) to As(V). Furthermore, we isolated representative pure cultures from both heterotrophic- and autotrophic-enriched cultures. The new isolates revealed new members of As(III)-oxidizing bacteria in the diversified bacterial community. This study highlights the natural process of As attenuation within river systems, showing that microcosms in river water can detoxify As under both organic-matter-rich and -deficient conditions. Additionally, we isolated the bacterial strains HTAs10 and ATAs5 from the microcosm which can be further investigated for potential use in As remediation systems. Our findings provide insights into the microbial ecology of As(III) oxidation in river ecosystems and provide a foundation for further investigations into the application of these bacteria for bioremediation. [ABSTRACT FROM AUTHOR]

The efficient removal of nitrate from industrial wastewater containing high concentrations of both sulfate and nitrate presents a major challenge in the field of water treatment. In this study, we investigated the use of an Upflow Anaerobic Sludge Blanket (UASB) reactor for the removal of nitrate from wastewater by gradually increasing the sulfate concentration (ranging from 1 g/L to 10 g/L) and the NO3−-N concentration (ranging from 30 mg/L to 300 mg/L). Through this approach, the activated sludge was successfully acclimated to tolerate high-sulfate conditions. The results demonstrated a remarkable NO3−-N removal capacity of 288 mg/L·d in wastewater with a high sulfate concentration of 10 g/L, leading to a nitrate removal efficiency exceeding 96.0%. The analysis of sulfate and sulfide concentrations, as well as the characterization of the microbial community, revealed the occurrence of autotrophic and heterotrophic denitrification processes in the reaction system. The autotrophic denitrifying bacteria found were Raoultella and Shinella, while the heterotrophic denitrifying bacteria included Klebsiella, Simplicispira, and Thauera. The organic carbon sources were found to be a critical factor influencing the denitrification performance of the system. Furthermore, the effects of different chemical oxygen demand (COD)/SO42− ratios (0.3, 0.5, and 1) were examined in wastewater containing a sulfate concentration of 10 g/L and a NO3−-N concentration of 300 mg/L. The results showed that increasing the COD/SO42− ratio enhanced the removal rate of NO3−-N, maintaining it above 98.0% when COD/SO42− was 1. Additionally, the enhancement of the sulfate reduction reaction in the system was observed, and the enrichment of heterotrophic microorganisms such as Megasphaera, Lactobacillus, and Buttiauxella was observed. [ABSTRACT FROM AUTHOR]

This work presents a methodology to evaluate the bioenergetic feasibility of alternative metabolic pathways for a given microbial conversion, optimising their energy yield and driving forces as a function of the concentration of metabolic intermediates. The tool, based on thermodynamic principles and multi-objective optimisation, accounts for pathway variants in terms of different electron carriers, as well as energy conservation (proton translocating) reactions within the pathway. The method also accommodates other constraints, some of them non-linear, such as the balance of conserved moieties. The approach involves the transformation of the maximum energy yield problem into a multi-objective mixed-integer linear optimisation problem which is then subsequently solved using the epsilon-constraint method, highlighting the trade-off between yield and rate in metabolic reactions. The methodology is applied to analyse several pathway alternatives occurring during propionate oxidation in anaerobic fermentation processes, as well as to the reverse TCA cycle pathway occurring during autotrophic microbial CO2 fixation. The results obtained using the developed methodology match previously reported literature and bring about insights into the studied pathways. Author summary: In this study we have developed a method that evaluates the feasibility of various metabolic pathways in microbes and finds the optimum concentrations of metabolic intermediates modes in terms of energy efficiency (yield) and driving forces (rate). The method is based on thermodynamic principles and uses multi-objective optimization to evaluate numerous different pathway variants, including the use of different electron carriers and energy conservation reactions. It also considers other constraints, such as the balance of conserved components. A complex mathematical problem is solved that maps the trade-off between yield and rate in the pathways evaluated. We applied this methodology to analyse alternative pathways in propionate oxidation and CO2 fixation by microbes. This research has potential applications in biotechnology and environmental studies, advancing our understanding of the trade-offs between energy efficiency and rate in different microbial pathways and allowing for the design of synthetic pathways for engineered organisms based on optimality principles. [ABSTRACT FROM AUTHOR]

Background and aims: Soil autotrophic microorganisms and plant primary production play crucial roles in soil carbon (C) cycling. However, the information remains limited to whether and how nitrogen (N) application influences the contribution of soil microbial C fixation to the soil organic C (SOC) pool. Methods: We investigated the effects of soil autotrophic bacterial communities on SOC storage and maize yield. A field experiment was conducted with four application rates of urea on the semiarid Loess Plateau, N application at 0 kg ha− 1 (N0), 100 kg ha− 1 (N1), 200 kg ha− 1 (N2), and 300 kg ha− 1 (N3), respectively. Results: Our results showed that SOC storage and maize yield were significantly increased by N application, but no significant SOC storage difference between N2 and N3 treatments, no further yield increase beyond 200 N kg ha− 1 application was observed. N application significantly impacted soil Calvin-Benson-Bassham (CBB) (cbbL) gene-carrying bacterial communities via changing soil pH, nitrate N, and soil water content. The diversity of soil autotrophic bacterial communities decreased with increasing rate of N application. We detected a high abundance of the autotrophic bacterial dominant genera Xanthobacter, Bradyrhizobium, Aminobacter, and Nitrosospira. The co-occurrence network of autotrophic bacteria contained four distinct modules. Structural equation modeling further indicated that the autotrophic bacterial communities had positive relationships with SOC storage and maize yield. Conclusions: Taken together, our results highlighted that N application stimulated the activity of soil autotrophic bacterial communities, contributing to an increase in SOC. The increase of SOC under N fertilization can stabilize soil fertility for maize production. [ABSTRACT FROM AUTHOR]

Since the beginning of unicellular life, dissimilation reactions of autotrophic sulfur bacteria have been a crucial part of the biogeochemical sulfur cycle on Earth. A wide range of sulfur oxidation states is reflected in the diversity of metabolic pathways used by sulfur-oxidizing bacteria. This metabolically and phylogenetically diverse group of microorganisms inhabits a variety of environments, including extreme environments. Although they have been of interest to microbiologists for more than 150 years, meso- and psychrophilic chemolithoautotrophic sulfur-oxidizing microbiota are less studied compared to the microbiota of hot springs. Several recent studies suggested that cold sulfur waters harbor unique, yet not described, bacterial taxa. [ABSTRACT FROM AUTHOR]

One of the important current issues of bioenergetics is the establishment of the thermodynamic limits of life. There is still no final understanding of what is the minimum value of the energy yield of a reaction that is sufficient to be used by an organism (the so-called "biological quantum of energy"). A reasonable model for determination of the minimal energy yield would be microorganisms capable of living on low-energy substrates, such as acetogenic prokaryotes. The most prominent metabolic feature of acetogens is autotrophic growth with molecular hydrogen and carbon dioxide as the substrates, which is hardly competitive in environments. Most probably, that is why only facultative autotrophic acetogens have been known so far. Here, we describe the first obligately autotrophic acetogenic bacterium Aceticella autotrophica gen. nov., sp. nov., strain 3443-3AcT. Phylogenetically, the new genus falls into a monophyletic group of heterotrophic bacteria of the genera Thermoanaerobacterium, Thermoanaerobacter, and Caldanaerobacter (hereinafter referred to as TTC group), where the sole acetogenic representative has so far been the facultatively autotrophic Thermoanaerobacter kivui. A. autotrophica and T. kivui both are acetogens employing energy-converting hydrogenase (Ech-acetogens) that are likely to have inherited the acetogenesis capacity vertically from common ancestor. However, their acetogenic machineries have undergone different adjustments by gene replacements due to horizontal gene transfers from different donors. Obligate autotrophy of A. autotrophica is associated with the lack of many sugar transport systems and carbohydrate catabolism enzymes that are present in other TTC group representatives, including T. kivui. [ABSTRACT FROM AUTHOR]

Summary: Cyanobacterial blooms pose a serious threat to public health due to the presence of cyanotoxins. Microcystin‐LR (MC‐LR) produced by Microcystis aeruginosa is the most common cyanotoxins. Due to the limitation of isolation, purification, and genetic manipulation techniques, it is difficult to study and verify in situ the biosynthetic pathways and molecular mechanisms of MC‐LR.We reassembled the biosynthetic gene cluster (mcy cluster) of MC‐LR in vitro by synthetic biology, designed and constructed the strong bidirectional promoter biPpsbA2, transformed it into Synechococcus 7942, and successfully expressed MC‐LR at a level of 0.006–0.018 fg cell−1 d−1.We found the expression of MC‐LR led to abnormal cell division and cellular filamentation, further using various methods proved that by irreversibly competing its GTP‐binding site, MC‐LR inhibits assembly of the cell division protein FtsZ.The study represents the first reconstitution and expression of the mcy cluster and the autotrophic production of MC‐LR in model cyanobacterium, which lays the foundation for resolving the microcystins biosynthesis pathway. The discovered role of MC‐LR in cell division reveals a mechanism of how blooming cyanobacteria gain a competitive edge over their nonblooming counterparts. [ABSTRACT FROM AUTHOR]

Dark CO2 fixation by bacteria is believed to be particularly important in oligotrophic ecosystems. However, only a few studies have characterized the role of bacterial dissolved inorganic carbon (DIC) fixation in global carbon dynamics. Therefore, this study quantified the primary production (PP), total bacteria dark CO2 fixation (TBDIC fixation), and heterotrophic bacterial production (HBP) in the warm and oligotrophic Red Sea using stable isotope labeling and cavity ring-down spectroscopy (13C-CRDS). Additionally, we assessed the contribution of bacterial DIC fixation (TBDIC %) relative to the total DIC fixation (TotalDIC fixation). Our study demonstrated that TBDIC fixation increased the TotalDIC fixation from 2.03 to 60.45 µg C L-1 d-1 within the photic zone, contributing 13.18 % to 71.68 % with an average value of 33.95 ± 0.02 % of the photic layer TotalDIC fixation. The highest TBDIC fixation values were measured at the surface and deep (400 m) water with an average value of 5.23 ± 0.45 µg C L-1 d-1, and 4.95 ± 1.33 µg C L-1 d-1, respectively. These findings suggest that the non-photosynthetic processes such as anaplerotic DIC reactions and chemo-autotrophic CO2 fixation extended to the entire oxygenated water column. On the other hand, the % of TBDIC contribution to TotalDIC fixation increased as primary production decreased (R² = 0.45, p <0.0001), suggesting the relevance of increased dark DIC fixation when photosynthetic production was low or absent, as observed in other systems. Therefore, when estimating the total carbon dioxide production in the ocean, dark DIC fixation must also be accounted as a crucial component of the carbon dioxide flux in addition to photosynthesis. [ABSTRACT FROM AUTHOR]