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As one of the ultimate products of hydrocarbon biodegradation, inorganic carbon always be used to evaluate hydrocarbon biodegradation rates in petroleum-hydrocarbon-contaminated (PHC) aquifers. The evaluation method was challenged because of the existence of carbon fixation microorganisms, which may uptake inorganic carbons and consequently cause the biodegradation rates to be underestimated. We wonder if there are carbon fixation microorganisms in PHC aquifers. Although an extremely limited number of carbon fixation microorganisms in PHC sites have been studied in previous studies, the vast majority of microorganisms that participate in carbon fixation have not been systematically identified. To systematically reveal carbon fixation microorganisms and their survival environmental conditions, high-throughput metagenomic sequencing technologies, which are characterized by culture-independent, unbiased, and comprehensive methods for the detection and taxonomic characterization of microorganisms, were introduced to analyze the groundwater samples collected from a PHC aquifer. Results showed that 1041 genera were annotated as carbon fixation microorganisms, which accounted for 49% of the total number of genera in the PHC aquifer. Carbon fixation genes involved in Calvin-Benson-Bassham (CBB), 3-hydroxy propionate (3HP), reductive tricarboxylic acid (rTCA), and Wood-Ljungdahl (WL) cycles accounted for 2%, 41%, 34%, and 23% of the total carbon fixation genes, respectively, and 3HP, rTCA, and WL can be deemed as the dominant carbon fixation pathways. Most of the identified carbon fixation microorganisms are potential hydrocarbon biodegraders, and the most abundant carbon fixation microorganisms, such as Microbacterium , Novosphingobium , and Reyranella , were just the most abundant microorganisms in the aquifer system. It's deduced that most of the microorganisms in the aquifer were facultative autotrophic, and undertaking the dual responsibilities of degrading hydrocarbons to inorganic carbon and uptaking inorganic carbon to biomass. [Display omitted] • Metagenomic analysis revealed highly diverse carbon fixation genes in a PHC aquifer. • 3HP, rTCA and WL cycles were the dominant carbon fixation pathways in the PHC aquifer. • Most of identified carbon fixation bacteria are potential hydrocarbon biodegraders. • Refreshed the carbon cycle knowledge in PHC aquifers. [ABSTRACT FROM AUTHOR]

Sulphur-oxidising autotrophic bacterial communities in deep biosphere from weathered ore samples from active gold mine Hodruša-Hámre, Slovakia were analysed using cultivation approach followed by DNA extraction, PCR amplification and 16S rRNA gene analyses. Indirect measurement of pH changes in cultivation media evidenced the presence of acidophilic bacteria with active production of acids. The decrease of pH was observed at the beginning of isolation and later pH in range of 1.5 – 2 was maintained in both, sulphuric acid and thiosulphate, media. The presence of homogenous population of gram-negative rods was proved by Gram staining. Molecular analyses have revealed that the population of sulphur-oxidising bacteria in gold mine is dominated by a single species of Aciditiobacillus genus, identified as A. albertensis, suggesting the low level of autotrophic bacteria diversity in deep deposits. For the first time this species was isolated from weathered rocks of a gold mine subsurface environment.

Low-cost photocatalysts are being developed for the conversion of visible light into H 2 and to drive CO 2 reduction. Hybrid photosynthesis is a promising approach to convert CO 2 and visible light into multicarbon compounds where a photocatalyst energizes the metabolism of an autotrophic microbe. Here, a heterostructure ZnSe/ZnS photocatalyst was synthesized by a simple one-pot method and evaluated for photocatalytic H 2 evolution (PHE) as well as for hybrid photosynthesis with the bioplastic-producing bacterium Ralstonia eutropha. ZnSe/ZnS nanoparticles exhibited a PHE 5.5 times higher than pure ZnSe. Photoluminescence and photoelectrochemical characterization of ZnSe/ZnS demonstrated more efficient charge separation probably caused by ZnS defects. Furthermore, ZnSe/ZnS improved 1.3 times bioplastic production from CO 2 by R. eutropha , which was not the case for pure ZnSe. These results show ZnSe/ZnS potential for both PHE as well as hybrid photosynthesis and provide insights on the photocatalytic reaction mechanisms involved when the two Zn-based materials are combined. [Display omitted] • A heterostructure ZnSe/ZnS photocatalyst was synthesized by a simple one-pot method. • H 2 evolution under visible light by ZnSe/ZnS was 5.5 times faster than pure ZnSe. • ZnSe/ZnS exhibited more efficient charge separation than pure ZnSe. • Under visible light, ZnSe/ZnS photoaugmented microbial PHB production from fructose. • ZnSe/ZnS also photoaugmented microbial PHB production from CO 2. [ABSTRACT FROM AUTHOR]

Soil autotrophic bacteria play a crucial role in regulating CO2 fixation and crop productivity. However, the information is limited to how fertilization amendments alter soil autotrophic bacterial community, crop yield, and carbon emission efficiency (CEE). Here, we estimated the impact of the structure and co-occurrence network of soil autotrophic bacterial community on maize yield and CEE. A long-term field experiment was conducted with five fertilization treatments in semiarid Loess Plateau, including no amendment (NA), chemical fertilizer (CF), chemical fertilizer plus commercial organic fertilizer (SC), commercial organic fertilizer (SM), and maize straw (MS). The results showed that fertilization amendments impacted the structure and network of soil Calvin–Benson–Bassham (CBB) (cbbL) gene-carrying bacterial community via changing soil pH and NO3–N. Compared with no amendment, the cbbL -carrying bacterial diversity was increased under the SC, SM, and MS treatments but decreased under the CF treatment. Soil autotrophic bacterial network contained distinct microbial modules that consisted of closely associated microbial species. We detected the higher abundances of soil cbbL -carrying bacterial genus Xanthobacter , Bradyrhizobium , and Nitrosospira. Structural equation modeling further suggested that the diversity, composition, and network of autotrophic bacterial community had strongly positive relationships with CEE and maize yield. Taken together, our results suggest that soil autotrophic bacterial community may drive crop productivity and CEE, and mitigate the atmospheric greenhouse effect. [ABSTRACT FROM AUTHOR]

• The addition of biochar improved humic substances formation and compost quality. • Biochar amendment promoted the degradation of organic matter and hemicellulose. • Biochar enriched the populations of cbbL -containing autotrophic microbes. • CO 2 sequestration was positively related to C/N, temperature and humic substances. The quality of compost is drastically reduced due to the loss of carbon, which negatively impacts the environment. Carbon emission reduction and carbon dioxide (CO 2) fixation have attracted much attention in composting research. In this study, the relationship between CO 2 emission, humic substances (HS) formation and cbbL -containing autotrophic microbes (CCAM) was analyzed by adding biochar during cow manure composting. The results showed that biochar can facilitate the degradation of organic matter (OM) and formation of HS, as well as reinforce the diversity and abundance of CCAM community, thereby promoting CO 2 fixation and reducing carbon loss during composting. High-throughput sequencing analysis revealed significant increase in Actinobacteriota and Proteobacteria abundance by 30.97 % and 10.48 %, respectively, thus increasing carbon fixation by 32.07 %. Additionally, Alpha diversity index increased significantly during thermophilic phase, while Shannon index increased by 143.12 % and Sobs index increased by 51.62 %. Redundancy analysis (RDA) indicated that CO 2 was positively correlated with C/N, temperature, HS and dissolved organic matter (DOM), while the abundance of Paeniclostridium , Corynebacterium , Bifidobacterium , Clostridium , Turicibacter and Romboutsia were positively correlated with temperature, CO 2 , C/N and E 2 /E 4 (p < 0.01). [ABSTRACT FROM AUTHOR]

BACKGROUND: The removal of biological nitrite from wastewater can occur by both heterotrophic and autotrophic bacteria. Autotrophic denitritation can be implemented by using different sulphur forms (e.g., S2−, S0 or S₂O₃2−) as electron donors, and there is no need for organic carbon availability, as is required in heterotrophic denitrification. This work investigated an alternative biochemical pathway for nitrite removal from synthetic wastewater with high nitrite content, using thiosulphate as electron donor. The process was examined for 170 days in three identical 1 L sequencing batch reactors (SBR) that were inoculated with filtrate originating from the aerobic filters of the desulphurization unit of a wastewater treatment plant (WWTP). RESULTS: The SBR units were able to remove approximately 98% of the initial nitrite concentration of 70–80 mg N L−1, operating under an HRT of 5d. The batch experiments showed autotrophic denitritation rates (NUR) with average values between 0.91 and 1.50 mg NO₂‐N gVSS−1 h−1 during the whole duration of the experiment, with a remarkable increase on the NUR after the initial lag time of the process, where rates of up to 4.74 mg NO₂‐N gVSS−1 h−1 were measured. CONCLUSION: The daily monitoring of the three SBR units showed that denitritation via thiosulphate can be effective enough for nitrite removal without carbon source addition. The lag phase of the process, as well as the loss of alkalinity and pH drop during denitritation, are disadvantages that can be counterbalanced with the cost savings resulting from not needing a carbon source addition when treating wastewater with low C/N ratio. © 2021 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

• Aquatic protists are a sustainable source for food grade omega-3. • Strain selection is important for efficient omega-3 rich oil production. • Development of a sustainable biorefinery model is required to reduce overall production costs. • Evaluation of food by-products and waste as alternative nutrients for protist cultivation. Biotechnological production of omega-3 polyunsaturated fatty acids (PUFAs) has become a commercial alternative to fish oil in the past twenty years. Compared to PUFA production by fatty fishes, that from microorganisms has increased due to its promising sustainability and high product safety and to increasing awareness in the expanding vegan market. Although autotrophic production by microalgae seems to be more sustainable in the long term, to date most of the microbial production of omega-3 is carried out under heterotrophic conditions using conventional fermentation technologies. The present review critically analyzes the main reasons for this discrepancy and reports on the recent advances and the most promising approaches for its future development in the context of sustainability and circular economy. [ABSTRACT FROM AUTHOR]

The recently isolated cyanobacterium Synechococcus elongatus UTEX 2973 (Syn2973) is characterized by a faster growth rate and greater tolerance to high temperature and high light, making it a good candidate chassis for autotrophic photosynthetic microbial cell factories. However, Syn2973 is sensitive to salt stress, making it urgently important to improve the salt tolerance of Syn2973 for future biotechnological applications. Glucosylglycerol, a compatible solute, plays an important role in resisting salt stress in moderate and marine halotolerant cyanobacteria. In this study, the salt tolerance of Syn2973 was successfully improved by introducing the glucosylglycerol (GG) biosynthetic pathway (OD750 improved by 24% at 60 h). In addition, the salt tolerance of Syn2973 was further enhanced by overexpressing the rate-limiting step of glycerol-3-phosphate dehydrogenase and downregulating the gene rfbA , which encodes UDP glucose pyrophosphorylase. Taken together, these results indicate that the growth of the end-point strain M-2522-GgpPS-drfbA was improved by 62% compared with the control strain M-pSI-pSII at 60 h under treatment with 0.5 M NaCl. Finally, a comparative metabolomic analysis between strains M-pSI-pSII and M-2522-GgpPS-drfbA was performed to characterize the carbon flux in the engineered M-2522-GgpPS-drfbA strain, and the results showed that more carbon flux was redirected from ADP-GLC to GG synthesis. This study provides important engineering strategies to improve salt tolerance and GG production in Syn2973 in the future. [ABSTRACT FROM AUTHOR]

Interactions between autotrophic and heterotrophic bacteria are fundamental for marine biogeochemical cycling. How global warming will affect the dynamics of these essential microbial players is not fully understood. The aims of this study were to identify the major groups of heterotrophic bacteria present in a Synechococcus culture originally isolated from the Red Sea and assess their joint responses to experimental warming within the metabolic ecology framework. A co-culture of Synechococcus sp. RS9907 and their associated heterotrophic bacteria, after determining their taxonomic affiliation by 16S rRNA gene sequencing, was acclimated and maintained in the lab at different temperatures (24–34°C). The abundance and cellular properties of Synechococcus and the three dominant heterotrophic bacterial groups (pertaining to the genera Paracoccus , Marinobacter , and Muricauda) were monitored by flow cytometry. The activation energy of Synechococcus , which grew at 0.94–1.38 d–1, was very similar (0.34 ± 0.02 eV) to the value hypothesized by the metabolic theory of ecology (MTE) for autotrophs (0.32 eV), while the values of the three heterotrophic bacteria ranged from 0.16 to 1.15 eV and were negatively correlated with their corresponding specific growth rates (2.38–24.4 d–1). The corresponding carrying capacities did not always follow the inverse relationship with temperature predicted by MTE, nor did we observe a consistent response of bacterial cell size and temperature. Our results show that the responses to future ocean warming of autotrophic and heterotrophic bacteria in microbial consortia might not be well described by theoretical universal rules. [ABSTRACT FROM AUTHOR]

[Display omitted] • A single biofilter reactor (BR) realized Partial nitrification coupled with anammox. • Different bacteria were partitioned along BR with big ratio of height to diameter. • Light organic suspended fillers were adopted to ensure the high BR not overweight. • TN removal percentage of 82.5 % was obtained in BR under the NLR of 2.0 kg/(m3·d). • 91.9 % NH 4 +-N could be removed from the influent of 800.0 mg/L when HRT in BR was 9.6 h. A biofilter reactor (BR) with large height-to-diameter ratio was developed for the continuous treatment of wastewater with high ammonia nitrogen and low carbon in this study. The BR integrated carbon oxidation, partial nitrification, and anammox process in a single-stage reactor and acquired an average removal rates of 91.9 % for NH 4 +-N and 82.5 % for TN when the nitrogen loading rate (NLR) reached 2.0 kg/(m3·d)) with the ammonia nitrogen of 800.0 ± 2.0 mg/L in the influent. The results revealed that nearly half of NH 4 +-N was stably converted into NO 2 −-N at the zone height of 0–40 cm in the reactor, which provided suitable conditions for the subsequent anammox process at the height of 80–160 cm. Meanwhile, high-throughput sequencing results further revealed that aerobic autotrophic bacteria were the main kind of bacteria at the zone height of 0–40 cm, whereas Candidatus_Brocadia were the main bacteria at the height of 80–160 cm. Thus, a BR with a large height-to-diameter ratio can combine the partial nitrification and anammox (PN/A) process in a single reactor, providing an effective technology for the treatment of high-ammonia-nitrogen wastewater. [ABSTRACT FROM AUTHOR]

Grazing by herbivorous protists contributes to structuring plankton communities through its effect on the growth, biomass, and competitiveness of prey organisms and also impacts the transfer of primary production towards higher trophic levels. Previous evidence shows that heterotrophic processes (grazing rates, g) are more sensitive to temperature than autotrophic ones (phytoplankton growth rates, μ) and also that small cells tend to be more heavily predated than larger ones; however, it remains unresolved how the interplay between changes in temperature and cell size modulates grazing pressure (i.e., g:μ ratio). We addressed this problem by conducting an experiment with four phytoplankton populations, from pico- to microphytoplankton, over a 12 °C gradient and in the presence/absence of a generalist herbivorous protist, Oxyrrhis marina. We found that highest g rates coincided with highest μ rates, which corresponded to intermediate cell sizes. There were no significant differences in either μ or g between the smallest and largest cell sizes considered. The g:μ ratio was largely independent of cell size and C:N ratios, and its thermal dependence was low although species-specific differences were large. We suggest that the similar g:μ found could be the consequence that the energetic demand imposed by rising temperatures would be a more important issue than the mechanical constriction to ingestion derived from prey cell size. Despite the difficulty of quantifying μ and g in natural planktonic communities, we suggest that the g:μ ratio is a key response variable to evaluate thermal sensitivity of food webs because it gives a more integrative view of trophic functioning than both rates separately. [ABSTRACT FROM AUTHOR]

The effect of the novel composite material LiNbO3@Fe3O4 on the nitrate removal, and Mn2+ oxidation efficiency by autotrophic denitrification strain Achromobacter sp. A14 was investigated in this study. The optimum conditions were tested by using five levels of initial Mn2+ concentrations (40, 60, 80, 100 and 120 mg/L), initial pH (5.0, 6.0, 7.0, 8.0 and 9.0) and temperature (20, 25, 30, 35 and 40°C). A maximal nitrate removal ratio of nearly 100% and a maximal Mn2+ oxidation ratio of 71.59% were simultaneously achieved at pH 7.0, 80 mg/L Mn2+ and 30°C by bacteria A14 with 300 mg/L LiNbO3@Fe3O4 as catalytic material. Biomaterial cycle testing indicated that the denitrification efficiency of bacteria A14 with LiNbO3@Fe3O4 remained steady after 10 batches. [ABSTRACT FROM AUTHOR]

Algae have long been acclaimed as the attractive renewable source for generating third-generation biofuels, particularly biodiesel. Under the present investigation, the trends of production of biomass and lipid during the autotrophic and heterotrophic growth of newly isolated blue-green algae, Leptolyngbya subtilis JUCHE1, were compared and correlated with the variation in C-sources. In the autotrophic and heterotrophic growth studies, CO2 and glycerol were respectively used as the inorganic and organic C-sources maintaining equivalence in the initial amount of carbon. Light was used as the source of energy in both cases. The concentration of CO2 in the feed gas stream was varied from 5 to 20% (% v/v). Equivalent quantity of carbon was supplied through glycerol during heterotrophic growth. Small-scale closed algal bioreactors were used for growing the algae at 37 °C and 2.5 kLux light illumination in batch mode for 0–4 days. Primarily, higher biomass production from glycerol compared with CO2 was observed. In case of photoautotrophic growth, the maximum values of biomass and lipid productivity, obtained at 15% CO2, were 0.1857 g/L/d and of 0.020 g/L/d respectively. The maximum biomass productivity of 0.2733 g/L/d was obtained for photoheterotrophic growth at a glycerol concentration equivalent to 15% CO2 (v/v). Under photoheterotrophic growth of Leptolyngbya subtilis JUCHE1, lipid productivity of 0.0702 g/L/d was obtained at glycerol concentration equivalent to 5% (v/v) CO2, which is 4.66-fold higher than that obtained under corresponding photoautotrophic condition. The "switch-over" from the autotrophy to the photoheterotrophy instigated the oleaginous anabolism and consequent lipid enrichment in L. subtilis JUCHE1, which can be extracted and converted to biodiesel. [ABSTRACT FROM AUTHOR]

The impact of changes in nitrogen (N) and phosphorus (P) availability on the trophic strategies of planktonic protists was evaluated in a disturbed Mediterranean lagoon (Biguglia lagoon, France) using short-term bioassays. Natural communities were collected in three periods, i.e., autumn, spring and summer, to address the influence of the different environmental conditions. The responses of autotrophic plankton communities to experimentally induced N and/or P limitations were assessed as changes in chlorophyll a (Chl a) concentrations and in the abundances of potentially mixotrophic protists taxa. We observed blooms (> 105 cells l−1) of nanoflagellates in autumn, and of phycocyanin-rich picocyanobacteria in summer. Communities showed a co-limitation by N and P at the three sampling periods, despite high N:P ratios in autumn and spring. The high abundances of potentially mixotrophic dinoflagellates during these periods suggest the involvement of alternative trophic pathways for their maintenance in the lagoon. After bioassay incubations using different nutrient enrichment treatments, we often observed reduced abundances of mixotrophic protists containing Chl a with a concomitant increased abundance of protists without Chl a. This indicates a loss of chloroplasts and photoautotrophic abilities in protists cells, possibly reflecting a shift towards heterotrophy that could be sustained by phagotrophy. [ABSTRACT FROM AUTHOR]

In marine and freshwater oxygen-deficient zones, the remineralization of sinking organic matter from the photic zone is central to driving nitrogen loss. Deep blooms of photosynthetic bacteria, which form the suboxic/anoxic chlorophyll maximum (ACM), widespread in aquatic ecosystems, may also contribute to the local input of organic matter. Yet, the influence of the ACM on nitrogen and carbon cycling remains poorly understood. Using a suite of stable isotope tracer experiments, we examined the transformation of nitrogen and carbon under an ACM (comprising of Chlorobiaceae and Synechococcales) and a non-ACM scenario in the anoxic zone of Lake Tanganyika. We find that the ACM hosts a tight coupling of photo/litho-autotrophic and heterotrophic processes. In particular, the ACM was a hotspot of organic matter remineralization that controlled an important supply of ammonium driving a nitrification-anammox coupling, and thereby played a key role in regulating nitrogen loss in the oxygen-deficient zone. Enigmatic blooms of phytoplankton in aquatic oxygen-deficient zones could exacerbate depletion of nitrogen. Here the authors perform stable isotope experiments on the oxygen-deficient waters of Lake Tanganyika in Africa, finding that blooms drive down fixed nitrogen and could expand as a result of climate change. [ABSTRACT FROM AUTHOR]

Little is known about the direct effects of microplastics (MPs) and their organic additives on marine bacteria, considering their role in the nutrient cycles, e.g., N-cycles through the N2-fixation, or in the microbial food web. To fill this gap of knowledge, we exposed marine bacteria, specifically diazotrophs, to pure MPs which differ in physical properties (e.g., density, hydrophobicity, and/or size), namely, polyethylene, polypropylene, polyvinyl chloride and polystyrene, and to their most abundant associated organic additives (e.g., fluoranthene, 1,2,5,6,9,10-hexabromocyclododecane and dioctyl-phthalate). Growth, protein overproduction, direct physical interactions between MPs and bacteria, phosphorus acquisition mechanisms and/or N2-fixation rates were evaluated. Cyanobacteria were positively affected by environmental and high concentrations of MPs, as opposed to heterotrophic strains, that were only positively affected with high concentrations of ~120 μm-size MPs (detecting the overproduction of proteins related to plastic degradation and C-transport), and negatively affected by 1 μm-size PS beads. Generally, the organic additives had a deleterious effect in both autotrophic and heterotrophic bacteria and the magnitude of the effect is suggested to be dependent on bacterial size. Our results show species-specific responses of the autotrophic and heterotrophic bacteria tested and the responses (beneficial: the "good," deleterious: the "bad" and/or both: the "double-sword") were dependent on the type and concentration of MPs and additives. This suggests the need to determine the threshold levels of MPs and additives concentrations starting from which significant effects can be observed for key microbial populations in marine systems, and these data are necessary for effective environmental quality control management. [ABSTRACT FROM AUTHOR]

Background: The majority of microbial fermentations are currently performed in the batch or fed-batch manner with the high process complexity and huge water consumption. The continuous microbial production can contribute to the green sustainable development of the fermentation industry. The co-culture systems of photo-autotrophic and heterotrophic species can play important roles in establishing the continuous fermentation mode for the bio-based chemicals production. Results: In the present paper, the co-culture system of Synechococcus elongates–Escherichia coli was established and put into operation stably for isoprene production. Compared with the axenic culture, the fermentation period of time was extended from 100 to 400 h in the co-culture and the isoprene production was increased to eightfold. For in depth understanding this novel system, the differential omics profiles were analyzed. The responses of BL21(DE3) to S. elongatus PCC 7942 were triggered by the oxidative pressure through the Fenton reaction and all these changes were linked with one another at different spatial and temporal scales. The oxidative stress mitigation pathways might contribute to the long-lasting fermentation process. The performance of this co-culture system can be further improved according to the fundamental rules discovered by the omics analysis. Conclusions: The isoprene-producing co-culture system of S. elongates–E. coli was established and then analyzed by the omics methods. This study on the co-culture system of the model S. elongates–E. coli is of significance to reveal the common interactions between photo-autotrophic and heterotrophic species without natural symbiotic relation, which could provide the scientific basis for rational design of microbial community. [ABSTRACT FROM AUTHOR]

Autotrophic nitrogen removal by anaerobic ammonium oxidizing (anammox) bacteria is an energy-efficient nitrogen removal process in wastewater treatment. However, full-scale deployment under mainstream conditions remains challenging for practitioners due to the high stress susceptibility of anammox bacteria towards fluctuations in dissolved oxygen (DO) and temperature. Here, we investigated the response of microbial biofilms with verified anammox activity to DO shocks under 20 °C and 14 °C. While pulse disturbances of 0.3 mg L−1 DO prompted only moderate declines in the NH4+ removal rates, 1.0 mg L−1 DO led to complete but reversible inhibition of the NH4+ removal activity in all reactors. Genome-centric metagenomics and metatranscriptomics were used to investigate the stress response on various biological levels. We show that temperature regime and strength of DO perturbations induced divergent responses from the process level down to the transcriptional profile of individual taxa. Community-wide gene expression differed significantly depending on the temperature regime in all reactors, and we found a noticeable impact of DO disturbances on genes involved in transcription, translation, replication and posttranslational modification at 20 °C but not 14 °C. Genome-centric analysis revealed that different anammox species and other key biofilm taxa differed in their transcriptional responses to distinct temperature regimes and DO disturbances. Niederdorfer et al. show that different anaerobic ammonium oxidizing (anammox) bacterial species and other key biofilm taxa vary in their transcriptional responses as a function of temperature and dissolved oxygen disturbances in an engineered ecosystem. This study highlights the links between microbial community stress response, individual stress response, and process level failure in anammox mainstream wastewater treatment. [ABSTRACT FROM AUTHOR]

Characterizing ecological relationships between viruses, bacteria and phytoplankton in the ocean is critical to understanding the ecosystem; however, these relationships are infrequently investigated together. To understand the dynamics of microbial communities and environmental factors in harmful algal blooms (HABs), we examined the environmental factors and microbial communities during Akashiwo sanguinea HABs in the Jangmok coastal waters of South Korea by metagenomics. Specific bacterial species showed complex synergistic and antagonistic relationships with the A. sanguinea bloom. The endoparasitic dinoflagellate Amoebophrya sp. 1 controlled the bloom dynamics and correlated with HAB decline. Among nucleocytoplasmic large DNA viruses (NCLDVs), two Pandoraviruses and six Phycodnaviruses were strongly and positively correlated with the HABs. Operational taxonomic units of microbial communities and environmental factors associated with A. sanguinea were visualized by network analysis: A. sanguinea–Amoebophrya sp. 1 (r =.59, time lag: 2 days) and A. sanguinea–Ectocarpus siliculosus virus 1 in Phycodnaviridae (0.50, 4 days) relationships showed close associations. The relationship between A. sanguinea and dissolved inorganic phosphorus relationship also showed a very close correlation (0.74, 0 day). Microbial communities and the environment changed dynamically during the A. sanguinea bloom, and the rapid turnover of microorganisms responded to ecological interactions. A. sanguinea bloom dramatically changes the environments by exuding dissolved carbohydrates via autotrophic processes, followed by changes in microbial communities involving host‐specific viruses, bacteria and parasitoids. Thus, the microbial communities in HAB are composed of various organisms that interact in a complex manner. [ABSTRACT FROM AUTHOR]

The Laguna Madre-Tamaulipas is the world's largest hypersaline lagoon and is equally located in south Texas, USA, and Tamaulipas, Mexico. Over 40% of its American surface area is covered by wind-tidal sand flats containing cyanobacteria as the major autotrophic component of the microbial community. A recent laboratory examination of these microbial mats revealed the presence of a boring, filamentous cyanobacterium which, in culture, 'drilled' through an agar substrate. The observed clockwise/counterclockwise rotation, gliding, and boring ability of the filaments was atypical for any known cyanobacterium. The isolate from Laguna Madre produces nine toxins that were originally described from both marine and freshwater habitats. Presence of a diverse array of bioactive metabolites in our unialgal culture agrees with earlier work demonstrating diverse toxin production by marine cyanobacteria. Initial comparison of this new taxon with its polyphasically closest genus, Oxynema, showed several morphological, physiological, and phylogenetic differences, warranting establishment of a new family Laspinemaceae, containing Perforafilum tunnelli gen. & sp. nov. [ABSTRACT FROM AUTHOR]

Phosphoketolase (PKET) pathway is predominant in cyanobacteria (around 98%) but current opinion is that it is virtually inactive under autotrophic ambient CO2 condition (AC-auto). This creates an evolutionary paradox due to the existence of PKET pathway in obligatory photoautotrophs. We aim to answer the paradox with the aid of bioinformatic analysis along with metabolic, transcriptomic, fluxomic and mutant data integrated into a multi-level kinetic model. We discussed the problems linked to neglected isozyme, pket2 (sll0529) and inconsistencies towards the explanation of residual flux via PKET pathway in the case of silenced pket1 (slr0453) in Synechocystis sp. PCC 6803. Our in silico analysis showed: (1) 17% flux reduction via RuBisCO for Δpket1 under AC-auto, (2) 11.2–14.3% growth decrease for Δpket2 in turbulent AC-auto, and (3) flux via PKET pathway reaching up to 252% of the flux via phosphoglycerate mutase under AC-auto. All results imply that PKET pathway plays a crucial role under AC-auto by mitigating the decarboxylation occurring in OPP pathway and conversion of pyruvate to acetyl CoA linked to EMP glycolysis under the carbon scarce environment. Finally, our model predicted that PKETs have low affinity to S7P as a substrate. [ABSTRACT FROM AUTHOR]

In ecology and population biology, logistic equation is widely applied for simulating the population of organisms. By combining the logistic model with the low-density effect called Allee effect, several variations of mathematical expressions have been proposed. The upper half of the work was dedicated to establish a novel equation for highly flexible density effect model with Allee threshold. Allee effect has been rarely observed in microorganisms with asexual reproduction despite of theoretical studies. According to the exploitation ecosystem hypotheses, plants are believed to be insensitive to Allee effect. Taken together, knowledge on the existence of low-density effect in photosynthetic microorganisms is required for redefining the ecological theories emphasizing the photosynthetic organisms as the basis for food chains. Therefore, in the lower half of the present article, we report on the possible Allee effect in photo-autotrophic organisms, namely, green paramecia, and cyanobacteria. Optically monitored growth of green paramecia was shown to be regulated by Allee-like weak low-density effect under photo-autotrophic and photo-heterotrophic conditions. Insensitiveness of wild type cyanobacteria (Synechocystis sp. Strain PCC6803) to low-density effect was confirmed, as consistent with our empirical knowledge. In contrast, a mutant line of PCC6803 impaired with a photosynthesis-related pxcA gene was shown to be sensitive to typical Allee's low-density effect (i.e. this line of cells failed to propagate at low cellular density while cells start logarithmic growth at relatively higher inoculating density). This is the first observation that single-gene mutation in an autotrophic organism alters the sensitivity to Allee effect. [ABSTRACT FROM AUTHOR]

With the goal of achieving carbon sequestration, emission reduction and cleaner production, biological methods have been employed to convert carbon dioxide (CO2) into fuels and chemicals. However, natural autotrophic organisms are not suitable cell factories due to their poor carbon fixation efficiency and poor growth rate. Heterotrophic microorganisms are promising candidates, since they have been proven to be efficient biofuel and chemical production chassis. This review first briefly summarizes six naturally occurring CO2 fixation pathways, and then focuses on recent advances in artificially designing efficient CO2 fixation pathways. Moreover, this review discusses the transformation of heterotrophic microorganisms into hemiautotrophic microorganisms and delves further into fully autotrophic microorganisms (artificial autotrophy) by use of synthetic biological tools and strategies. Rapid developments in artificial autotrophy have laid a solid foundation for the development of efficient carbon fixation cell factories. Finally, this review highlights future directions toward large-scale applications. Artificial autotrophic microbial cell factories need further improvements in terms of CO2 fixation pathways, reducing power supply, compartmentalization and host selection. [ABSTRACT FROM AUTHOR]

Gas fermentation by autotrophic bacteria, such as clostridia, offers a sustainable path to numerous bioproducts from a range of local, highly abundant, waste and low-cost feedstocks, such as industrial flue gases or syngas generated from biomass or municipal waste. Unfortunately, designing and engineering clostridia remains laborious and slow. The ability to prototype individual genetic part function, gene expression patterns, and biosynthetic pathway performance in vitro before implementing designs in cells could help address these bottlenecks by speeding up design. Unfortunately, a high-yielding cell-free gene expression (CFE) system from clostridia has yet to be developed. Here, we report the development and optimization of a high-yielding (236 ± 24 μg/mL) batch CFE platform from the industrially relevant anaerobe, Clostridium autoethanogenum. A key feature of the platform is that both circular and linear DNA templates can be applied directly to the CFE reaction to program protein synthesis. We demonstrate the ability to prototype gene expression, and quantitatively map aerobic cell-free metabolism in lysates from this system. We anticipate that the C. autoethanogenum CFE platform will not only expand the protein synthesis toolkit for synthetic biology, but also serve as a platform in expediting the screening and prototyping of gene regulatory elements in non-model, industrially relevant microbes. • Developed cell-free gene expression system from Clostridium autoethanogenum. • Optimized batch protein expression titers to be more than 100 μg/mL. • Mapped aerobic cell-free metabolism in lysates from this cell-free system. • Showed potential for genetic part and codon optimization screening. [ABSTRACT FROM AUTHOR]

Six CO2 fixation pathways are known to operate in photoautotrophic and chemoautotrophic microorganisms. Here, we describe chemolithoautotrophic growth of the sulphate-reducing bacterium Desulfovibrio desulfuricans (strain G11) with hydrogen and sulphate as energy substrates. Genomic, transcriptomic, proteomic and metabolomic analyses reveal that D. desulfuricans assimilates CO2 via the reductive glycine pathway, a seventh CO2 fixation pathway. In this pathway, CO2 is first reduced to formate, which is reduced and condensed with a second CO2 to generate glycine. Glycine is further reduced in D. desulfuricans by glycine reductase to acetyl-P, and then to acetyl-CoA, which is condensed with another CO2 to form pyruvate. Ammonia is involved in the operation of the pathway, which is reflected in the dependence of the autotrophic growth rate on the ammonia concentration. Our study demonstrates microbial autotrophic growth fully supported by this highly ATP-efficient CO2 fixation pathway. There are several pathways for CO2 fixation in photoautotrophic and chemoautotrophic microorganisms. Here, the authors provide experimental demonstration for the operation of the reductive glycine pathway in a natural microorganism, Desulfovibrio desulfuricans. [ABSTRACT FROM AUTHOR]

Microbes exchange electrons with their extracellular environment via direct or indirect means. This exchange is bidirectional and supports essential microbial oxidation–reduction processes, such as respiration and photosynthesis. The microbial capacity to use electrons from insoluble electron donors, such as redox-active minerals, poised electrodes, or even other microbial cells is called extracellular electron uptake (EEU). Autotrophs with this capability can thrive in nutrient and soluble electron donor-deficient environments. As primary producers, autotrophic microbes capable of EEU greatly impact microbial ecology and play important roles in matter and energy flow in the biosphere. In this review, we discuss EEU-driven autotrophic metabolisms, their mechanism and physiology, and highlight their ecological, evolutionary, and biotechnological implications. [ABSTRACT FROM AUTHOR]

In linear food chains, resource and predator control produce positive and negative correlations, respectively, between biomass at adjacent trophic levels. These simple relationships become more complex in food webs that contain alternative food chains of unequal lengths. We have used a "minimum" model for the microbial part of the pelagic food web that has three such food chains connecting free mineral nutrients to copepods: via diatoms, autotrophic flagellates, and heterotrophic bacteria. Trophic cascades from copepods strongly modulates the balance between the three pathways and, therefore, the functionality of the microbial food web in services such as food production for higher trophic levels, DOM degradation, and ocean carbon sequestration. The result is a theoretical framework able to explain, not only apparent conflicts in Arctic mesocosm experiments, but also biogeochemical features of the Mediterranean. Here, the fundamental difference between Arctic and Mediterranean microbial food webs is the way they are predator driven by seasonal migration of large copepods in the Arctic, but resource driven due to the anti-estuarine circulation in the Mediterranean. In this framework, global change effects on microbial ecosystem functions are more like to come indirectly through changes in these drivers than through direct temperature effects on the microbes. [ABSTRACT FROM AUTHOR]

The goal of the present work was to study the oxidation of sulfide mineral pyrrhotite by members of microbial groups predominant in biohydrometallurgical processes (mixotrophic iron- and sulfur-oxidizing bacterium Sulfobacillus thermosulfidooxidans strain VKMV 1269T, autotrophic sulfur-oxidizing bacterium Acidithiobacillus caldus strain MBC-1, and heterotrophic iron- and sulfur-oxidizing archaeon Acidiplasma sp. strain MBA-1) to evaluate the role of microorganisms with different physiological properties in the leaching of this mineral. It was shown that pyrrhotite was most actively leached by the sulfur-oxidizing strain Acidithiobacillus caldus MBC-1, as well as by mixed cultures in which this strain was present: S. thermosulfidooxidans VKMV 1269T + A. caldus MBC-1 and Acidiplasma sp. MBA-1 + A. caldus MBC-1. These cultures leached 70, 43, and 60% of pyrrhotite, respectively, after 30 days of the experiment. In experiments with pure cultures S. thermosulfidooxidans VKMV 1269T, Acidiplasma sp. MBA-1 and a mixed culture S. thermosulfidooxidans VKMV 1269T + Acidiplasma sp. MBA-1, the rates of pyrrhotite leaching were significantly lower: 29, 37 and 30%, respectively. An experiment on sulfur biooxidation by pure cultures of the studied microorganisms demonstrated that A. caldus strain MBC-1 was the most active sulfur oxidizer. Thus, it was shown that the bioleaching of pyrrhotite was carried out mainly by sulfur-oxidizing microorganisms, with sulfur biooxidation as the most important process. Active biooxidation of the Fe2+ ion by iron-oxidizing microorganisms did not increase activity of pyrrhotite oxidation, but, on the contrary, led to inhibition of pyrrhotite leaching. Thus, active biooxidation of sulfur, which is formed during the leaching of pyrrhotite, was a factor determining the leaching rate for this sulfide mineral. [ABSTRACT FROM AUTHOR]

Euglena gracilis is a green photosynthetic microalga that swims using its flagellum. This species has been used as a model organism for over half a century to study its metabolism and the mechanisms of its behavior. The development of mass-cultivation technology has led to E. gracilis application as a feedstock in various products such as foods. Therefore, breeding of E. gracilis has been attempted to improve the productivity of this feedstock for potential industrial applications. For this purpose, a characteristic that preserves the microalgal energy e.g., reduces motility, should be added to the cultivars. The objective of this study was to verify our hypothesis that E. gracilis locomotiondefective mutants are suitable for industrial applications because they save the energy required for locomotion. To test this hypothesis, we screened for E. gracilis mutants from Fe-ion-irradiated cell suspensions and established a mutant strain, M3-3 ZFeL, which shows defects in flagellum formation and locomotion. The mutant strain exhibits a growth rate comparable to that of the wild type when cultured under autotrophic conditions, but had a slightly slower growth under heterotrophic conditions. It also stores 1.6 times the amount of paramylon, a crystal of β-1,3-glucan, under autotrophic culture conditions, and shows a faster sedimentation compared with that of the wild type, because of the deficiency in mobility and probably the high amount of paramylon accumulation. Such characteristics make E. gracilis mutant cells suitable for costeffective mass cultivation and harvesting. [ABSTRACT FROM AUTHOR]

• The RubisCO-producing microbes widely existed in composting. • The composition and diversity of autotrophic bacterial communities were identified. • The cbbL and cbbM gene abundances in composting were comparable to that in soil. • Autotrophic bacterial composition was mainly related with temperature, C/N and pH. The CO 2 fixation by autotrophic microbes has an important significance for improving carbon sequestration in composting. In this work, the succession of autotrophic CO 2 -fixing bacterial communities was investigated using quantitative PCR and high-throughput sequencing of the ribulose-1,5-bisphosphate carboxylase/oxygenase genes (cbbL and cbbM). The results presented that the number of autotrophic CO 2 -fixing bacteria was comparable to that in the soil, and most species have not been classified into known bacterial groups, only part of them was assigned into Proteobacteria and Actinobacteria. Phylogenetic analysis displayed that the dominant known cbbL -containing bacteria were Allochromatium vinosum , Rhodobacter sphaeroides , Nitrobacter winogradskyi , Paracoccus yeei and Porphyrobacter sp. CACIAM 03H1 , while the dominant known cbbM -containing bacteria were Sulfuritalea hydrogenivorans , Pseudomonas resinovorans , Achromobacter xylosoxidans , Sphingopyxis macrogoltabida and Thermomonospora curvata. In addition, canonical correspondence analysis showed that the evolution of autotrophic CO 2 -fixing bacterial communities was greatly affected by physico-chemical parameters such as temperature, C/N and pH. [ABSTRACT FROM AUTHOR]

A respirometric method for the kinetic modeling of ammonium‐oxidizing bacteria (AOB) and nitrite‐oxidizing bacteria (NOB) was implemented in two membrane bioreactor (MBRA and MBRB) systems. These biological systems worked at mixed liquor suspended solids concentration of about 6.6 g L−1. MBRA worked at 6 hr of hydraulic retention time (HRT) and 20.7°C, while the operational conditions for MBRB were 9.5 hr of HRT and 14.7°C. Experimental data were fitted to the kinetic model with R2 values of.9320 and.9250 for MBRA and MBRB, respectively. Both systems showed similar performances regarding organic matter and nitrogen removal. However, MBRB showed highest rates of carbon source degradation and net heterotrophic bacteria growth, and MBRA had highest rates of nitrogen source degradation and net autotrophic bacteria growth. This last system was characterized by values for YAOB, YNOB, μm,AOB and μm,NOB of 1.1749 mgVSS mgN−1, 0.6473 mgVSS mgN−1, 0.3664 hr−1 and 0.1823 hr−1, respectively. [ABSTRACT FROM AUTHOR]

Isotopically nonstationary metabolic flux analysis (INST-MFA) provides a versatile platform to quantitatively assess in vivo metabolic activities of autotrophic systems. By applying INST-MFA to recombinant aldehyde-producing cyanobacteria, we identified metabolic alterations that correlated with increased strain performance in order to guide rational metabolic engineering. We identified four reactions adjacent to the pyruvate node that varied significantly with increasing aldehyde production: pyruvate kinase (PK) and acetolactate synthase (ALS) fluxes were directly correlated with product formation, while pyruvate dehydrogenase (PDH) and phosphoenolpyruvate carboxylase (PPC) fluxes were inversely correlated. Overexpression of enzymes for PK or ALS did not result in further improvements to the previous best-performing strain, while downregulation of PDH expression (through antisense RNA expression) or PPC flux (through expression of the reverse reaction, phosphoenolpyruvate carboxykinase) provided significant improvements. These results illustrate the potential of INST-MFA to enable a systematic approach for iterative identification and removal of pathway bottlenecks in autotrophic host cells. • INST-MFA was used to identify gene targets for increasing aldehyde production. • PDH and PPC fluxes were inversely correlated with productivity. • Knockdown of PDH increased aldehyde productivity by ~50%. • Overexpression of PEPCK increased titer by ~60% but inhibited growth. • Flux analysis provides a systematic approach to guide iterative strain improvement. [ABSTRACT FROM AUTHOR]

Autotrophic microorganisms catalyze the entry of dissolved inorganic carbon (DIC; = CO2 + HCO3− + CO32−) into the biological component of the global carbon cycle, despite dramatic differences in DIC abundance and composition in their sometimes extreme environments. "Cyanobacteria" are known to have CO2 concentrating mechanisms (CCMs) to facilitate growth under low CO2 conditions. These CCMs consist of carboxysomes, containing enzymes ribulose 1,5-bisphosphate oxygenase and carbonic anhydrase, partnered to DIC transporters. CCMs and their DIC transporters have been studied in a handful of other prokaryotes, but it was not known how common CCMs were beyond "Cyanobacteria". Since it had previously been noted that genes encoding potential transporters were found neighboring carboxysome loci, α-carboxysome loci were gathered from bacterial genomes, and potential transporter genes neighboring these loci are described here. Members of transporter families whose members all transport DIC (CHC, MDT and Sbt) were common in these neighborhoods, as were members of the SulP transporter family, many of which transport DIC. 109 of 115 taxa with carboxysome loci have some form of DIC transporter encoded in their genomes, suggesting that CCMs consisting of carboxysomes and DIC transporters are widespread not only among "Cyanobacteria" , but also among members of " Proteobacteria" and " Actinobacteria". [ABSTRACT FROM AUTHOR]

Coastal zones of Antarctica harbor rich but highly variable phytoplankton communities. The mechanisms that control the dynamics of these communities are not well defined. Here we elucidate the mechanisms that drive seasonal species succession, based on algal photophysiological characteristics and environmental factors. For this, phytoplankton community structure together with oceanographic parameters was studied over a 5‐year period (2012–2017) at Rothera Station at Ryder Bay (Western Antarctic Peninsula). Algal pigment patterns and photophysiological studies based on fluorescence analyses were combined with data from the Rothera Time‐Series program. Considerable interannual variation was observed, related to variations in wind‐mixing, ice cover and an El Niño event. Clear patterns in the succession of algal classes became manifest when combining the data collected over the five successive years. In spring, autotrophic flagellates with a high light affinity were the first to profit from increasing light and sea ice melt. These algae most likely originated from sea‐ice communities, stressing the role of sea ice as a seeding vector for the spring bloom. Diatoms became dominant towards summer in more stratified and warmer surface waters. These communities displayed significantly lower photoflexibility than spring communities. There are strong indications for mixotrophy in cryptophytes, which would explain much of their apparently random occurrence. Climate models predict continuing retreat of Antarctic sea‐ice during the course of this century. For the near‐future we predict that the marginal sea‐ice zone will still harbor significant communities of haptophytes and chlorophytes, whereas increasing temperatures will mainly be beneficial for diatoms. [ABSTRACT FROM AUTHOR]

The influence of nanostructural-biocolloidal processes in sea sediments on rheological properties of concentrated iron–aluminosilicate dispersions is studied. As shown, the change of their rheological properties significantly influences on catastrophic phenomena in sea turbiditic–pelitic sediments. Considering the laws of physicochemical geomechanics (PCHG), the causes and mechanisms of transformation of dispersions and sediments in the conditions of catastrophic phenomena are revealed. As established, such phenomena start by reaching the mechanical-stress level, which corresponds to the beginning of the transformation from elastic-into-plastic deformation of dispersions and sediments. Under the act of different factors, the elastic deformation first proceeds to laminar ultraanomal and then to hyperanomal plastic flow, and after all, to a turbulent flow through the dilatant, rheopexic, and thixotropic stages. It happens in conditions of sliding of huge masses of sediments and soils with the formation of catastrophic turbidity currents. As shown for the first time, such phenomena are controlled not as much by the contact nanostructural interactions in dispersions caused by colloidal, nanochemical, and geomechanical processes, but by biocolloidal interactions caused initially by bacterial and then by chemical reactions. In the last processes, iron-reducing and autotrophic bacteria, which produce thousands of amphiphilic surfactants of peptide series, play the important role. Such surfactants accelerate the dispersion of sediment minerals up to nanolevel, according to PCHG the laws, due to the acceleration of nanodestruction of iron–aluminosilicates by the mechanism of autohydrational dispersion. [ABSTRACT FROM AUTHOR]

Serpentinite-hosted systems represent modern-day analogs of early Earth environments. In these systems, water-rock interactions generate highly alkaline and reducing fluids that can contain hydrogen, methane, and low-molecular-weight hydrocarbons-potent reductants capable of fueling microbial metabolism. In this study, we investigated the microbiota of Hakuba Happo hot springs (∼50°C; pH∼10.5–11), located in Nagano (Japan), which are impacted by the serpentinization process. Analysis of the 16S rRNA gene amplicon sequences revealed that the bacterial community comprises Nitrospirae (47%), "Parcubacteria" (19%), Deinococcus-Thermus (16%), and Actinobacteria (9%), among others. Notably, only 57 amplicon sequence variants (ASV) were detected, and fifteen of these accounted for 90% of the amplicons. Among the abundant ASVs, an early-branching, uncultivated actinobacterial clade identified as RBG-16-55-12 in the SILVA database was detected. Ten single-cell genomes (average pairwise nucleotide identity: 0.98–1.00; estimated completeness: 33–93%; estimated genome size: ∼2.3 Mb) that affiliated with this clade were obtained. Taxonomic classification using single copy genes indicates that the genomes belong to the actinobacterial class-level clade UBA1414 in the Genome Taxonomy Database. Based on metabolic pathway predictions, these actinobacteria are anaerobes, capable of glycolysis, dissimilatory nitrate reduction and CO2 fixation via the Wood–Ljungdahl (WL) pathway. Several other genomes within UBA1414 and two related class-level clades also encode the WL pathway, which has not yet been reported for the Actinobacteria phylum. For the Hakuba actinobacterium, the energy metabolism related to the WL pathway is likely supported by a combination of the Rnf complex, group 3b and 3d [NiFe]-hydrogenases, [FeFe]-hydrogenases, and V-type (H+/Na+ pump) ATPase. The genomes also harbor a form IV ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) complex, also known as a RubisCO-like protein, and contain signatures of interactions with viruses, including clustered regularly interspaced short palindromic repeat (CRISPR) regions and several phage integrases. This is the first report and detailed genome analysis of a bacterium within the Actinobacteria phylum capable of utilizing the WL pathway. The Hakuba actinobacterium is a member of the clade UBA1414/RBG-16-55-12, formerly within the group "OPB41." We propose to name this bacterium ' Candidatus Hakubanella thermoalkaliphilus.' [ABSTRACT FROM AUTHOR]

Polyhydroxyalkanoates (PHA), polyesters accumulated by numerous prokaryotes in the form of intracellular granules, have been for decades considered being predominantly storage molecules. However, numerous recent discoveries revealed and emphasized their complex biological role for microbial cells. Most of all, it was repeatedly reported and confirmed that the presence of PHA granules in prokaryotic cells enhances stress resistance and robustness of microbes against various environmental stress factors such as high or low temperature, freezing, oxidative, and osmotic pressure. It seems that protective mechanisms of PHA granules are associated with their extraordinary architecture and biophysical properties as well as with the complex and deeply interconnected nature of PHA metabolism. Therefore, this review aims at describing novel and unexpected properties of PHA granules with respect to their contribution to stress tolerance of various prokaryotes including common mesophilic heterotrophic bacteria, but also extremophiles or photo-autotrophic cyanobacteria. Key points: • PHA granules present in bacterial cells reveal unique properties and functions. • PHA enhances stress robustness of bacterial cells. [ABSTRACT FROM AUTHOR]

• A bioreactor was designed to cultivate C.necator under a safe environment and high pressure. • Cultivations led to growth and production of C. necator up to 3 g DCW L-1 and 3.5 g L-1 isopropanol. • First demonstration of g L-1-scale molecule production from autotrophic engineered bacteria. A bioreactor was designed to provide high gas mass transfer to reach cell and product titres in the g L-1 level from CO 2 for realistic, laboratory scale, engineered autotrophic strain evaluation. The design was based on independent CO 2 , H 2 and air inputs and the ability to operate at high pressures. The bioreactor configuration and cultivation strategy enabled growth of Cupriavidus necator strains for long periods, to reach over 3 g L-1 dry cell weight. No negative impact of the high pressure was observed on viability of the strains up to more than 4 bar overpressure. The cultivation was then carried out using an engineered isopropanol producing strain; in this case, 3.5 g L-1 isopropanol was obtained from CO 2 as the sole carbon source. This is the first reported demonstration of a successful production from engineered bacteria of product in the g L-1 range on CO 2 , raising the prospect of future development of CO 2 -based bioprocesses. [ABSTRACT FROM AUTHOR]

Background: Cyanobacteria, a group of photosynthetic prokaryotes, are being increasingly explored for direct conversion of carbon dioxide to useful chemicals. However, efforts to engineer these photoautotrophs have resulted in low product titers. This may be ascribed to the bottlenecks in metabolic pathways, which need to be identified for rational engineering. We engineered the recently reported, fast-growing and robust cyanobacterium, Synechococcus elongatus PCC 11801 to produce succinate, an important platform chemical. Previously, engineering of the model cyanobacterium S. elongatus PCC 7942 has resulted in succinate titer of 0.43 g l−1 in 8 days. Results: Building on the previous report, expression of α-ketoglutarate decarboxylase, succinate semialdehyde dehydrogenase and phosphoenolpyruvate carboxylase yielded a succinate titer of 0.6 g l−1 in 5 days suggesting that PCC 11801 is better suited as host for production. Profiling of the engineered strains for 57 intermediate metabolites, a number of enzymes and qualitative analysis of key transcripts revealed potential flux control points. Based on this, we evaluated the effects of overexpression of sedoheptulose-1,7-bisphosphatase, citrate synthase and succinate transporters and knockout of succinate dehydrogenase and glycogen synthase A. The final construct with seven genes overexpressed and two genes knocked out resulted in photoautotrophic production of 0.93 g l−1 succinate in 5 days. Conclusion: While the fast-growing strain PCC 11801 yielded a much higher titer than the model strain, the efficient photoautotrophy of this novel isolate needs to be harnessed further for the production of desired chemicals. Engineered strains of S. elongatus PCC 11801 showed dramatic alterations in the levels of several metabolites suggesting far reaching effects of pathway engineering. Attempts to overexpress enzymes deemed to be flux controlling led to the emergence of other potential rate-limiting steps. Thus, this process of debottlenecking of the pathway needs to be repeated several times to obtain a significantly superior succinate titer. [ABSTRACT FROM AUTHOR]

Gymnodinium smaydae is a fast-growing mixotrophic dinoflagellate. This study investigated whether light intensity (0–346 µmol photons m−2 s−1) and temperature (5–35 °C) affect the autotrophic or mixotrophic growth rate or ingestion rate of Gymnodinium smaydae GSSH1005. At all light intensities tested, G. smaydae GSSH1005 showed negative autotrophic growth rates, but positive mixotrophic growth rates when feeding on Heterocapsa rotundata. However, both autotrophic and mixotrophic growth rates were significantly affected by light intensity. The mixotrophic growth rates at 0–6 µmol photons m−2 s−1 were 0.67–0.72 day−1; they increased up to 1.28 day−1 at 58 µmol photons m−2 s−1, but became saturated at higher light intensities. The ingestion rates were also significantly affected by light intensity. The maximum ingestion rate of 2.3 ng C predator−1 day−1 was achieved at 58 µmol photons m−2 s−1. Although the autotrophic growth rates were negative at all temperatures tested, the mixotrophic growth rates were positive at 10–32 °C. Both autotrophic and mixotrophic growth rates were significantly affected by temperature. The maximum mixotrophic growth rate of 1.55 day−1 was noted at 25 °C. The ingestion rates were also significantly affected by temperature. The maximum ingestion rate of 4.2 ng C predator−1 day−1 was noted at 32 °C. Therefore, both light intensity and temperature can affect the population dynamics of G. smaydae GSSH1005. [ABSTRACT FROM AUTHOR]

A novel pigmented bacterium, initially identified as 11E, was isolated from a site historically known to have various iron-related ores. Phylogenetic analysis of this bacterial strain showed that it belongs to Serratia marcescens. This pigmented S. marcescens 11E cultured individually with glucose, acetate, and glycerol as electron donors along with the soluble electron acceptor iron (Fe) (III) citrate offered a large reduction extent (45.3 %, 31.4 %, and 13.5 %, respectively). On the other hand, when iron oxide (Fe2O3) is used as electron acceptor, the pigmented strain produced a null reduction extent. Surprisingly, the absence of prodigiosin on the bacterial surface (non-pigmented strain) resulted in a large reduction extent of the non-soluble iron form (20–49%). All these extents were comparable and, in some cases, superior to those presented in the literature. Additionally, in the present study, it was found that anthraquinone sulfonate (AQS) stimulated Fe(III) reduction of soluble and non-soluble Fe species only with pigmented S. marcescens. In contrast, in the culture media with the non-pigmented strain, the presence of AQS did not stimulate the Fe(III) reduction. These results suggest that the pigmented phenotype of S. marcescens 11E may perform non-soluble Fe(III) reduction by electron shuttling. In contrast, for the non-pigmented phenotype of this bacterium, non-soluble Fe(III) reduction seems to proceed by direct contact. Our study demonstrates that this bacterium may be used in bioreduction process of heavy metals or as a biocatalyst in bioelectrochemical devices. [ABSTRACT FROM AUTHOR]

Iron- and sulfur-oxidizing auto-, mixo- and heterotrophic bacteria and archaea dominate in the bioleaching of pyrite from sulfide ores and concentrates both in natural conditions and in biohydrometallurgical processes. The goal of the present work was to study the oxidation of pyrite, the most widespread sulfide mineral, by representatives of microbial groups predominant in biohydrometallurgical processes (mixotrophic iron- and sulfur-oxidizing bacterial strain Sulfobacillus thermosulfidooxidans VKMB1269T, autotrophic sulfur-oxidizing bacterial strain Acidithiobacillus caldus MBC-1, and heterotrophic iron- and sulfur-oxidizing strain of archaea Acidiplasma sp. MBA-1) to evaluate the potential importance of different groups of microorganisms, and to determine the role of interspecies interactions in the population during pyrite oxidation. It was shown that pyrite was most actively leached by the strain of the mixotrophic bacterium S. thermosulfidooxidans VKMB 1269T, in the case when the medium was supplemented with organic substrates. In the experiment with a pure culture of strain VKMV 1269T in a medium with 0.02% yeast extract, 17% of pyrite was leached in 30 days, while in experiments with pure cultures of A. caldus MBC-1 and Acidiplasma sp. MBA-1, less than 1.5% of pyrite were leached. Significantly better results were obtained using mixed cultures of iron-oxidizing strains and A. caldus MBC-1: the rate of pyrite leaching was 26–28%. Moreover, in experiments with a mixed culture of S. thermosulfidooxidans VKMB 1269T and A. caldus MBC-1, addition of an organic carbon source (yeast extract) did not affect the rate of pyrite leaching (25–26%). The highest (38%) leaching rate was in the experiments with a pure culture of S. thermosulfidooxidans VKMV 1269T with periodic addition of yeast extract to the medium: 0.02% at the beginning of the experiment, as well as on days 10 and 20. Thus, in laboratory conditions it was shown that the greatest role in the process of pyrite oxidation was played by the bacterial strain of the genus Sulfobacillus, but its activity was largely dependent on availability of an organic carbon source in the medium, which may be represented by yeast extract or exometabolites of autotrophic bacteria present in the community of microorganisms performing pyrite leaching from sulfide ores and concentrates. [ABSTRACT FROM AUTHOR]

Yeast and microalgae are microorganisms with widely diverging physiological and biotechnological properties. Accordingly, their fields of applications diverge: yeasts are primarily applied in processes related to fermentation, while microalgae are used for the production of high-value metabolites and green technologies such as carbon capture. Heterotrophic–autotrophic systems and synthetic ecology approaches have been proposed as tools to achieve stable combinations of such evolutionarily unrelated species. We describe an entirely novel synthetic ecology-based approach to evolve co-operative behaviour between winery wastewater isolates of the yeast Saccharomyces cerevisiae and microalga Chlorella sorokiniana. The data show that biomass production and mutualistic growth improved when co-evolved yeast and microalgae strains were paired together. Combinations of co-evolved strains displayed a range of phenotypes, including differences in amino acid profiles. Taken together, the results demonstrate that biotic selection pressures can lead to improved mutualistic growth phenotypes over relatively short time periods. [ABSTRACT FROM AUTHOR]

In this work, a down-flow fixed bed anaerobic biofilm reactor filled by biological ceramsites were prepared to remove the high concentration of NO3− (> 20 g/L) from nuclear industry wastewaters. The effects of hydraulic retention time, the concentration of NO3−, the molar ratio of C/N and temperature on the removal efficiencies of NO3− were investigated. The results showed that the removal rate of NO3− with the initial concentration of 6 g/L can reach 99% or more by controlling the hydraulic retention time at 0.75 h, the molar ratio of C/N at 1.5 and the temperature over 18 °C. In the process, the NO2− was not accumulated, and the autotrophic denitrifying bacteria grow well in anaerobic biofilm reactors, proving a usable method for removing the high concentration NO3− from nuclear industrial wastewaters. [ABSTRACT FROM AUTHOR]

The dynamics of diatoms and dinoflagellates have been monitored for many decades at the Helgoland Roads Long-Term Ecological Research site and are relatively well understood. In contrast, small-sized eukaryotic microbes and their community changes are still much more elusive, mainly due to their small size and uniform morphology, which makes them difficult to identify microscopically. By using next-generation sequencing, we wanted to shed light on the Helgoland planktonic community dynamics, including nano- and picoplankton, during a spring bloom. We took samples from March to May 2016 and sequenced the V4 region of the 18S rDNA. Our results showed that mixotrophic and heterotrophic taxa were more abundant than autotrophic diatoms. Dinoflagellates dominated the sequence assemblage, and several small-sized eukaryotic microbes like Haptophyta, Choanoflagellata, Marine Stramenopiles and Syndiniales were identified. A diverse background community including taxa from all size classes was present during the whole sampling period. Five phases with several communities were distinguished. The fastest changes in community composition took place in phase 3, while the communities from phases 1 to 5 were more similar to each other despite contrasting environmental conditions. Synergy effects of next-generation sequencing and traditional methods may be exploited in future long-term observations. [ABSTRACT FROM AUTHOR]

Domestication of CO2-fixation became a worldwide priority enhanced by the will to convert this greenhouse gas into fuels and valuable chemicals. Because of its high stability, CO2-activation/fixation represents a true challenge for chemists. Autotrophic microbial communities, however, perform these reactions under standard temperature and pressure. Recent discoveries shine light on autotrophic acetogenic bacteria and hydrogenotrophic methanogens, as these anaerobes use a particularly efficient CO2-capture system to fulfill their carbon and energy needs. While other autotrophs assimilate CO2 via carboxylation followed by a reduction, acetogens and methanogens do the opposite. They first generate formate and CO by CO2-reduction, which are subsequently fixed to funnel the carbon toward their central metabolism. Yet their CO2-reduction pathways, with acetate or methane as end-products, constrain them to thrive at the "thermodynamic limits of Life". Despite this energy restriction acetogens and methanogens are growing at unexpected fast rates. To overcome the thermodynamic barrier of CO2-reduction they apply different ingenious chemical tricks such as the use of flavin-based electron-bifurcation or coupled reactions. This mini-review summarizes the current knowledge gathered on the CO2-fixation strategies among acetogens. While extensive biochemical characterization of the acetogenic formate-generating machineries has been done, there is no structural data available. Based on their shared mechanistic similarities, we apply the structural information obtained from hydrogenotrophic methanogens to highlight common features, as well as the specific differences of their CO2-fixation systems. We discuss the consequences of their CO2-reduction strategies on the evolution of Life, their wide distribution and their impact in biotechnological applications. [ABSTRACT FROM AUTHOR]

• The paper presents a gas phase controller for autotrophic cultivations independent of metabolic information of the strain cultivated. • As a basic component, a feedforward disturbance rejection based on highly varying estimated gas transfer rates is used to unburden the controller. • This controller allows for running closed-loop controlled fermentations with a new strain without performing prior experiments. By this, enough cells can be produced for further biological studies. Additionally, informative data is obtained for modeling of the biotic part for a new strain. • Results are shown for the wild type strain of Ralstonia eutropha and two mutants cultivated with an explosive gas mixture of H 2 , O 2 and CO 2. This paper presents a control architecture suitable for autotrophic cultivations in a stirred tank reactor feeding a gas mixture of H 2 /CO 2 /O 2. No metabolic information about the cultivated strain is required for the gas phase controller, which can also be used as part of the overall control for the entire process. A gain-scheduled MIMO-PI controller connected to an adaptive feedforward disturbance rejection is proposed. The latter exploits the estimated gas transfer rates of a Kalman filter solely based on a description of the non-biotic processes occurring. Thus, without further knowledge of the autotrophic strain, experiments can be run to generate data and to develop a process model including strain-specific biological details. The wild-type strain H16 of Ralstonia eutropha and two mutants, HF805 and H798, are used to demonstrate how this can be done. [ABSTRACT FROM AUTHOR]