Differences of heterotrophic 13CO2 assimilation by Pseudomonas knackmussii strain B13 and Rhodococcus opacus 1CP and potential impact on biomarker stable isotope probing

Single-cell analysis reveals an active and heterotrophic microbiome in the Guaymas Basin deep subsurface with significant inorganic carbon fixation by heterotrophs

The marine subsurface is a long-term sink of atmospheric carbon dioxide with significant implications for climate on geologic timescales. Subsurface microbial cells can either enhance or reduce carbon sequestration in the subsurface, depending on their metabolic lifestyle. However, the activity of subsurface microbes is rarely measured. Here, we used nanoscale secondary ion mass spectrometry (nanoSIMS) to quantify anabolic activity in 3,203 individual cells from the thermally altered deep subsurface in the Guaymas Basin, Mexico (3-75 m below the seafloor, 0-14°C). We observed that a large majority of cells were active (83%-100%), although the rates of biomass generation were low, suggesting cellular maintenance rather than doubling. Mean single-cell activity decreased with increasing sediment depth and temperature and was most strongly correlated with porewater sulfate concentrations. Intracommunity heterogeneity in microbial activity decreased with increasing sediment depth and age. Using a dual-isotope labeling approach, we determined that all active cells analyzed were heterotrophic, deriving the majority of their cellular carbon from organic sources. However, we also detected inorganic carbon assimilation in these heterotrophic cells, likely via processes such as anaplerosis, and determined that inorganic carbon contributes at least 5% of the total biomass carbon in heterotrophs in this community. Our results demonstrate that the deep marine biosphere at Guaymas Basin is largely active and contributes to subsurface carbon cycling primarily by not only assimilating organic carbon but also fixing inorganic carbon. Heterotrophic assimilation of inorganic carbon may be a small yet significant and widespread underappreciated source of labile carbon in the global subsurface.

IMPORTANCE

The global subsurface is the largest reservoir of microbial life on the planet yet remains poorly characterized. The activity of life in this realm has implications for long-term elemental cycling, particularly of carbon, as well as how life survives in extreme environments. Here, we recovered cells from the deep subsurface of the Guaymas Basin and investigated the level and distribution of microbial activity, the physicochemical drivers of activity, and the relative significance of organic versus inorganic carbon to subsurface biomass. Using a sensitive single-cell assay, we found that the majority of cells are active, that activity is likely driven by the availability of energy, and that although heterotrophy is the dominant metabolism, both organic and inorganic carbon are used to generate biomass. Using a new approach, we quantified inorganic carbon assimilation by heterotrophs and highlighted the importance of this often-overlooked mode of carbon assimilation in the subsurface and beyond.

Emerging bio-capture strategies for greenhouse gas reduction: Navigating challenges towards carbon neutrality

Greenhouse gas emissions are significantly contributing to climate change, posing one of the serious threats to our planet. Addressing these emissions urgently is imperative to prevent irreversible planetary changes. One effective long-term mitigation strategy is achieving carbon neutrality. Although numerous countries aim for carbon neutrality by 2050, only a few are on track to realize this ambition. Existing technological solutions, including chemical absorption, cryogenic separation, and membrane separation, are available but tend to be costly and time intensive. Bio-capture methods present a promising opportunity in greenhouse gas mitigation research. Recent developments in biotechnology for capturing greenhouse gases have demonstrated both effectiveness and long-term benefits. This review emphasizes the recent advancements in bio-capture techniques, showcasing them as dependable and economical solutions for carbon neutrality. The article briefly outlines various bio-capture methods and underscores their potential for industrial application. Moreover, it investigates into the challenges faced when integrating bio-capture with carbon capture and storage technology. The study concludes by exploring the recent trends and prospective enhancements in ecosystem revitalization and industrial decarbonization through green conversion techniques, reinforcing the path towards carbon neutrality.

Metagenomic analysis of the effects of salinity on microbial community and functional gene diversity in glacial meltwater estuary, Ny-Alesund, Arctic

Due to the inflow of meltwater from the Midre Lovénbreen glacier upstream of Kongsfjorden, the nutrient concentration of Kongsfjorden change from the estuary to the interior of the fjord. Our objective was to explore the changes in bacterial community structure and metabolism-related genes from the estuary to fjord by metagenomic analysis. Our data indicate that glacial meltwater input has altered the physicochemical properties of the fjords, with a significant effect, in particular, on fjords salinity, thus altering the relative abundance of some specific bacterial groups. In addition, we suggest that the salinity of a fjord is an important factor affecting the abundance of genes associated with the nitrogen and sulfur cycles in the fjord. Changes in salinity may affect the relative abundance of microbial populations that carry metabolic genes, thus affecting the relative abundance of genes associated with the nitrogen and sulfur cycles.

Improved Assessment of Soil Nonextractable Residues of the Pyrethroid Insecticide Cyphenothrin

The metabolic fate of pyrethroid insecticide cyphenothrin (1) [(RS)-α-cyano-3-phenoxybenzyl (1RS)-cis-trans-2,2-dimethyl-3-(2-methylprop-1-enyl)cyclopropanecarboxylate] in soils was investigated using ¹⁴C-labeled (1R)-cis/trans isomers at the cyclopropane ring. Both isomers degraded with half-lives of 19.0-47.4 days, and 48.9-56.0% and 27.5-38.7% of the applied radioactivity (AR) were mineralized to CO₂ and incorporated into nonextractable residues (NER), respectively, after 120 days at 20 °C. NER analyses revealed 37.5-42.2% (cis-1) and 44.9-54.1% (trans-1) of each residue at 30/120 days were comprised of ¹⁴C-amino acids (AAs) as microbial products. Assuming that 50% of microbial biomass is AAs, it was estimated that 11.3-22.9%AR (cis-1, 75.0-84.4% of NER) and 13.9-30.4%AR (trans-1, 89.8-108.2% of NER) were nonhazardous biogenic NER (bio-NER), while type I/II xenobiotic NER (xeno-NER) characterized by silylation was insignificant at 0.9-1.0%/2.8-3.3%AR (cis-1). Detailed ¹⁴C-AA quantitation indicated a high relevance of the tricarboxylic acid cycle and pyruvate pathway during bio-NER formation, offering new insights into the microbial assimilation of the chrysanthemic moiety.

Active metabolism and biomass dynamics of biocrusts are shaped by variation in their successional state and seasonal energy sources

Seasonal growth and changes in biomass within communities are the core of ecosystem dynamics. Biocrusts play a prominent role as pioneers in dryland soils. However, the seasonal dynamics of biocrusts remain poorly resolved. In this study, we collected biocrusts across a successional gradient (cyanobacteria, cyanolichen, chlorolichen, and moss-dominated) from southeastern Tengger Desert (China) during the summer and autumn seasons, and explored seasonal changes in metabolism and biomass using multi-omics approaches. We found that Cyanobacteria and Ascomycota were the dominant active taxa and both exhibited higher abundances in autumn. We also found that the dominant primary producers in biocrusts strongly affected community-wide characteristics of metabolism. Along with seasonal differences in light energy utilization, utilization of inorganic energy sources exhibited higher expression in the summer while for organic sources, in the autumn. We found that overall metabolism was significantly regulated by the ratio of intracellular to extracellular polymer degradation, and affected by NO₃^-, PO₄^3- and EC (in the summer)/NO₂^- (in the autumn). In summary, biocrust growth varied with seasonal variation in light energy utilization and complementary chemical energy sources, with the most suitable season varying with biocrust successional type.

DNA- and RNA-SIP Reveal Nitrospira spp. as Key Drivers of Nitrification in Groundwater-Fed Biofilters

Nitrification, the oxidative process converting ammonia to nitrite and nitrate, is driven by microbes and plays a central role in the global nitrogen cycle. Our earlier investigations based on 16S rRNA and amoA amplicon analysis, amoA quantitative PCR and metagenomics of groundwater-fed biofilters indicated a consistently high abundance of comammox Nitrospira Here, we hypothesized that these nonclassical nitrifiers drive ammonia-N oxidation. Hence, we used DNA and RNA stable isotope probing (SIP) coupled with 16S rRNA amplicon sequencing to identify the active members in the biofilter community when subjected to a continuous supply of NH₄ ⁺ or NO₂ ^- in the presence of ¹³C-HCO₃ ^- (labeled) or ¹²C-HCO₃ ^- (unlabeled). Allylthiourea (ATU) and sodium chlorate were added to inhibit autotrophic ammonia- and nitrite-oxidizing bacteria, respectively. Our results confirmed that lineage II Nitrospira dominated ammonia oxidation in the biofilter community. A total of 78 (8 by RNA-SIP and 70 by DNA-SIP) and 96 (25 by RNA-SIP and 71 by DNA-SIP) Nitrospira phylotypes (at 99% 16S rRNA sequence similarity) were identified as complete ammonia- and nitrite-oxidizing, respectively. We also detected significant HCO₃ ^- uptake by Acidobacteria subgroup10, Pedomicrobium, Rhizobacter, and Acidovorax under conditions that favored ammonia oxidation. Canonical Nitrospira alone drove nitrite oxidation in the biofilter community, and activity of archaeal ammonia-oxidizing taxa was not detected in the SIP fractions. This study provides the first in situ evidence of ammonia oxidation by comammox Nitrospira in an ecologically relevant complex microbiome.IMPORTANCE With this study we provide the first in situ evidence of ecologically relevant ammonia oxidation by comammox Nitrospira in a complex microbiome and document an unexpectedly high H₁₃CO₃ ^- uptake and growth of proteobacterial and acidobacterial taxa under ammonia selectivity. This finding raises the question of whether comammox Nitrospira is an equally important ammonia oxidizer in other environments.

Significance of Fe(II) and environmental factors on carbon-fixing bacterial community in two paddy soils

The seasonal flooding and drainage process affect the paddy soils, the existence of the iron state either Fe(III) or Fe(II) is the main redox system of paddy soil. Its morphological transformation affects the redox nature of paddy soils, which also affects the distribution of bacterial community diversity. This study based on molecular biological methods (qPCR, Illumina MiSeq sequencing technique) to investigate the effect of Fe(II) and environmental factors on cbbM genes containing carbon fixing microbes. Both Eh5 and pH were reduced with Fe(II) concentrations. The Fe(II) addition significantly affects the cbbM gene copy number in both texture soils. In loamy soil, cbbM gene copy number increased with high addition of Fe(II), while both low and high concentrations significantly reduced the cbbM gene copy number in sandy soil. Chemotrophic bacterial abundance significantly increased by 79.7% and 54.8% with high and low Fe(II) addition in loamy soil while in sandy soil its abundance decreased by 53% and 54% with the low and high Fe(II) accumulation. The phototrophic microbial community increased by 37.8% with low Fe(II) concentration and decreased by 16.2% with a high concentration in loamy soil, while in sandy soil increased by 21% and 14.3% in sandy soil with low and high Fe(II) addition. Chemoheterotrophic carbon fixing bacterial abundance decreased with the Fe(II) accumulation in both soil textures in loamy soil its abundance decreased by 5.8% and 24.8%, while in sand soil 15.7% and 12.8% with low and high Fe(II) concentrations. The Fe(II) concentration and soil textures maybe two of the major factors to shape the bacterial community structure in paddy soils. These results provide a scientific basis for management of paddy soil fertility and it can be beneficial to take measures to ease the greenhouse gases effect.

Insights into the Metabolism of Oleaginous Rhodococcus spp

Some species belonging to the Rhodococcus genus, such as Rhodococcus opacus, R. jostii, and R. wratislaviensis, are known to be oleaginous microorganisms, since they are able to accumulate triacylglycerols (TAG) at more than 20% of their weight (dry weight). Oleaginous rhodococci are promising microbial cell factories for the production of lipids to be used as fuels and chemicals. Cells could be engineered to create strains capable of producing high quantities of oils from industrial wastes and a variety of high-value lipids. The comprehensive understanding of carbon metabolism and its regulation will contribute to the design of a reliable process for bacterial oil production. Bacterial oleagenicity requires an integral configuration of metabolism and regulatory processes rather than the sole existence of an efficient lipid biosynthesis pathway. In recent years, several studies have been focused on basic aspects of TAG biosynthesis and accumulation using R. opacus PD630 and R. jostii RHA1 strains as models of oleaginous bacteria. The combination of results obtained in these studies allows us to propose a metabolic landscape for oleaginous rhodococci. In this context, this article provides a comprehensive and integrative view of different metabolic and regulatory attributes and innovations that explain the extraordinary ability of these bacteria to synthesize and accumulate TAG. We hope that the accessibility to such information in an integrated way will help researchers to rationally select new targets for further studies in the field.

Effect of temperature, pH and total organic carbon variations on microbial turnover of 13C315N-glyphosate in agricultural soil

Glyphosate is the best-selling and the most-used broad-spectrum herbicide worldwide. Microbial conversion of glyphosate to CO2 and biogenic non-extractable residues (bioNER) leads to its complete degradation. The degradation of glyphosate may vary in different soils and it depends on environmental conditions and soil properties. To date, the influence of temperature, soil pH and total organic carbon (TOC) on microbial conversion of glyphosate to bioNER has not been investigated yet. The pH or TOC of an agricultural original soil (pH 6.6, TOC 2.1%) was modified using sulfuric acid or farmyard manure (FYM), respectively. Each treatment: original (I), 3% TOC (II), 4% TOC (III), pH 6.0 (IV) and pH 5.5 (V) was amended with 13C315N-glyphosate and incubated at 10 °C, 20 °C and 30 °C for 39 days. The temperature was the main factor controlling the mineralization and the extractable 13C315N-glyphosate, whereas higher TOC content and lower pH resulted in enhanced formation of 13C-bioNER. After 39 days the cumulative mineralization of 13C-glyphosate was in the range of 12-22% (10 °C), 37-47% (20 °C) and 43-54% (30 °C). Extractable residues of 13C-glyphosate were in the range of 10-21% (10 °C) and 4-10% (20 °C and 30 °C); whereas those of 15N-glyphosate were as follows 20-32% (10 °C) and 12-25% (20 °C and 30 °C). The 13C-NER comprised about 53-69% of 13C-mass balance in soils incubated at 10 °C, but 40-50% in soils incubated at 20 °C and 30 °C. The 15N-NER were higher than the 13C-NER and varied between 62% and 74% at 10 °C, between 53% and 81% at 20 °C and 30 °C. A major formation of 13C-bioNER (72-88% of 13C-NER) at 20 °C and 30 °C was noted in soil amended with FYM. An increased formation of 15N-bioNER (14-17% of 15N-NER) was also observed in FYM-amended soil. The xenobiotic 15N-NER had a major share within the 15N-NER and thus need to be considered when assessing the environmental risk of glyphosate-NER.

Unraveling microbial turnover and non-extractable residues of bromoxynil in soil microcosms with 13C-isotope probing

Bromoxynil is a widely used nitrile herbicide applied to maize and other cereals in many countries. To date, still little is known about bromoxynil turnover and the structural identity of bromoxynil non-extractable residues (NER) which are reported to occur in high amounts. Therefore, we investigated the microbial turnover of ¹³C-labeled bromoxynil for 32 days. A focus was laid on the estimation of biogenic NER based on the turnover of ¹³C into amino acids (AA). At the end, 25% of ¹³C₆-bromoxynil equivalents were mineralized, 2% assigned to extractable residues and 72.5% to NER. Based on 12% in the ¹³C-total AA and an assumed share of AA of 50% in microbial biomass we arrived at 24% of total ¹³C-biogenic NER. About 33% of the total ¹³C-NER could thus be explained by ¹³C-biogenic NER; 67% was unknown and by definition xenobiotic NER with potential for toxicity. The ¹³C label from ¹³C₆-bromoxynil was mainly detected in the humic acids (28.5%), but significant amounts were also found in non-humics (17.6%), fulvic acids (13.2%) and humins (12.7%). The ¹³C-total amino acids hydrolyzed from humic acids, humins and fulvic acids amounted to 5.2%, 6.1% and 1.2% of ¹³C₆-bromoxynil equivalents, respectively, corresponding to total ¹³C-biogenic NER amounts of 10.4%, 12.2% and 2.4%. The humins contained mostly ¹³C-biogenic NER, whereas the humic and fulvic acids may be dominated by the xenobiotic NER. Due to the high proportion of unknown ¹³C-NER and particularly in the humic and fulvic acids, future studies should focus on the detailed characterization of these fractions.

Transformation of metamitron in water-sediment systems: Detailed insight into the biodegradation processes

Metamitron and its main metabolite desamino-metamitron are frequently detected in surface waters. To date, there are no studies targeting metamitron degradation in water-sediment systems. Therefore, the aim of this study was to trace the fate of metamitron in a water-sediment system using ¹³C-isotope labeling. Mineralization of metamitron was high and accounted for 49% of ¹³C₆-metamitron equivalents at the end. In contrast, only 8.7% of ¹³C₆-metamitron equivalents were mineralized in the water only system demonstrating the key role of sediment for biodegradation. Metamitron disappeared from the water on day 40 and was completely removed from the sediment on day 80. This agrochemical was utilized as carbon source by microorganisms as shown by the incorporation of the ¹³C label into microbial amino acids and finally into biogenic residues. The latter amounted to 24% of ¹³C₆-metamitron equivalents at the end. However, 17% of ¹³C₆-metamitron equivalents were detected in xenobiotic non-extractable residues (NER) with a release potential and delayed risk for the environment. Metamitron was degraded via two pathways, initially via 4-(dimethylimino)-3-methyl-6-phenyl-1,2,4-triazin-5(4H)-one, which might be related to growth, and later via desamino-metamitron, which can be attributed to starvation.

Exploring eukaryotic formate metabolisms to enhance microbial growth and lipid accumulation

BACKGROUND

C1 substrates (such as formate and methanol) are promising feedstock for biochemical/biofuel production. Numerous studies have been focusing on engineering heterologous pathways to incorporate C1 substrates into biomass, while the engineered microbial hosts often demonstrate inferior fermentation performance due to substrate toxicity, metabolic burdens from engineered pathways, and poor enzyme activities. Alternatively, exploring native C1 pathways in non-model microbes could be a better solution to address these challenges.

RESULTS

An oleaginous fungus, Umbelopsis isabellina, demonstrates an excellent capability of metabolizing formate to promote growth and lipid accumulation. By co-feeding formate with glucose at a mole ratio of 3.9:1, biomass and lipid productivities of the culture in 7.5 L bioreactors were improved by 20 and 70%, respectively. 13C-metabolite analysis, genome annotations, and enzyme assay further discovered that formate not only provides an auxiliary energy source [promoting NAD(P)H and ATP] for cell anabolism, but also contributes carbon backbones via folate-mediated C1 pathways. More interestingly, formate addition can tune fatty acid profile and increase the portion of medium-chain fatty acids, which would benefit conversion of fungal lipids for high-quality biofuel production. Flux balance analysis further indicates that formate co-utilization can power microbial metabolism to improve biosynthesis, particularly on glucose-limited cultures.

CONCLUSION

This study demonstrates Umbelopsis isabellina's strong capability for co-utilizing formate to produce biomass and enhance fatty acid production. It is a promising non-model platform that can be potentially integrated with photochemical/electrochemical processes to efficiently convert carbon dioxide into biofuels and value-added chemicals.

Identification of degradation routes of metamitron in soil microcosms using 13C-isotope labeling

Metamitron is one of the most commonly used herbicide in sugar beet and flower bulb cultures. Numerous laboratory and field studies on sorption and degradation of metamitron were performed. Detailed biodegradation studies in soil using ¹³C-isotope labeling are still missing. Therefore, we aimed at providing a detailed turnover mass balance of ¹³C₆-metamitron in soil microcosms over 80 days. In the biotic system, metamitron mineralized rapidly, and ¹³CO₂ finally constituted 60% of the initial ¹³C₆-metamitron equivalents. In abiotic control experiments CO₂ rose to only 7.4% of the initial ¹³C₆-metamitron equivalents. The ¹³C label from ¹³C₆-metamitron was incorporated into microbial amino acids that were ultimately stabilized in the soil organic matter forming presumably harmless biogenic residues. Finally, ¹³C label from ¹³C₆-metamitron was distributed between the ¹³CO₂ and the ¹³C-biogenic residues indicating nearly complete biodegradation. The parallel increase of ¹³C-alanine, ¹³C-glutamate and ¹³CO₂ indicates that metamitron was initially biodegraded via the desamino-metamitron route suggesting its relevance in the growth metabolism. In later phases of biodegradation, the "Rhodococcus route" was indicated by the low ¹³CO₂ evolution and the high relevance of the pyruvate pathway, which aims at biomolecule synthesis and seems to be related to starvation. This is a first report on the detailed degradation route of metamitron in soil.

Characterization of key triacylglycerol biosynthesis processes in rhodococci

Oleaginous microorganisms have considerable potential for biofuel and commodity chemical production. Under nitrogen-limitation, Rhodococcus jostii RHA1 grown on benzoate, an analog of lignin depolymerization products, accumulated triacylglycerols (TAGs) to 55% of its dry weight during transition to stationary phase, with the predominant fatty acids being C16:0 and C17:0. Transcriptomic analyses of RHA1 grown under conditions of N-limitation and N-excess revealed 1,826 dysregulated genes. Genes whose transcripts were more abundant under N-limitation included those involved in ammonium assimilation, benzoate catabolism, fatty acid biosynthesis and the methylmalonyl-CoA pathway. Of the 16 atf genes potentially encoding diacylglycerol O-acyltransferases, atf8 transcripts were the most abundant during N-limitation (~50-fold more abundant than during N-excess). Consistent with Atf8 being a physiological determinant of TAG accumulation, a Δatf8 mutant accumulated 70% less TAG than wild-type RHA1 while atf8 overexpression increased TAG accumulation 20%. Genes encoding type-2 phosphatidic acid phosphatases were not significantly expressed. By contrast, three genes potentially encoding phosphatases of the haloacid dehalogenase superfamily and that cluster with, or are fused with other Kennedy pathway genes were dysregulated. Overall, these findings advance our understanding of TAG metabolism in mycolic acid-containing bacteria and provide a framework to engineer strains for increased TAG production.

Stable Isotope Probing Approaches to Study Anaerobic Hydrocarbon Degradation and Degraders

Stable isotope probing (SIP) techniques have become state-of-the-art in microbial ecology over the last 10 years, allowing for the targeted detection and identification of organisms, metabolic pathways and elemental fluxes active in specific processes within complex microbial communities. For studying anaerobic hydrocarbon-degrading microbial communities, four stable isotope techniques have been used so far: DNA/RNA-SIP, PLFA (phospholipid-derived fatty acids)-SIP, protein-SIP, and single-cell-SIP by nanoSIMS (nanoscale secondary ion mass spectrometry) or confocal Raman microscopy. DNA/RNA-SIP techniques are most frequently applied due to their most meaningful phylogenetic resolution. Especially using ¹³C-labeled benzene and toluene as model substrates, many new hydrocarbon degraders have been identified by SIP under various electron acceptor conditions. This has extended the current perspective of the true diversity of anaerobic hydrocarbon degraders relevant in the environment. Syntrophic hydrocarbon degradation was found to be a common mechanism for various electron acceptors. Fundamental concepts and recent advances in SIP are reflected here. A discussion is presented concerning how these techniques generate direct insights into intrinsic hydrocarbon degrader populations in environmental systems and how useful they are for more integrated approaches in the monitoring of contaminated sites and for bioremediation.

A simple separation method for downstream biochemical analysis of aquatic microbes

In order to study the chemical composition of aquatic microbes it is necessary to obtain completely separated fractions of subpopulations. Size separation by filtration is usually unsuccessful because the smaller group of organisms contaminates the larger fractions due to being trapped on filter surfaces of nominally much larger pore sizes. Here we demonstrate that a simple sucrose density separation method allowed us to separate microorganisms of even subtle size differences and to determine their bulk biochemical composition (proteins, polysaccharides+nucleic acids, and lipids). Both autotrophs and heterotrophs (through anaplerotic pathways) were labeled with (14)C-bicarbonate for biochemical fractionation. We provided proof of concept that eukaryotic microbes could be cleanly separated from prokaryotes in cultures and in field samples, enabling detection of differences in their biochemical makeup. We explored methodological issues regarding separation mechanisms, fixation, and pre-concentration via tangential flow filtration of oligotrophic marine waters where abundances of microorganisms are comparably low. By selecting an appropriate centrifugal force, two processes (i.e., isopycnal and rate-zonal separation) can be exploited simultaneously resulting in finely-separated density fractions, which also resulted in size separation. Future applications of this method include exploration of the stoichiometric, biochemical and genetic differences among subpopulations of microbes in a wide variety of aquatic environments.

Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells

Microbial communities are essential to the function of virtually all ecosystems and eukaryotes, including humans. However, it is still a major challenge to identify microbial cells active under natural conditions in complex systems. In this study, we developed a new method to identify and sort active microbes on the single-cell level in complex samples using stable isotope probing with heavy water (D2O) combined with Raman microspectroscopy. Incorporation of D2O-derived D into the biomass of autotrophic and heterotrophic bacteria and archaea could be unambiguously detected via C-D signature peaks in single-cell Raman spectra, and the obtained labeling pattern was confirmed by nanoscale-resolution secondary ion MS. In fast-growing Escherichia coli cells, label detection was already possible after 20 min. For functional analyses of microbial communities, the detection of D incorporation from D2O in individual microbial cells via Raman microspectroscopy can be directly combined with FISH for the identification of active microbes. Applying this approach to mouse cecal microbiota revealed that the host-compound foragers Akkermansia muciniphila and Bacteroides acidifaciens exhibited distinctive response patterns to amendments of mucin and sugars. By Raman-based cell sorting of active (deuterated) cells with optical tweezers and subsequent multiple displacement amplification and DNA sequencing, novel cecal microbes stimulated by mucin and/or glucosamine were identified, demonstrating the potential of the nondestructive D2O-Raman approach for targeted sorting of microbial cells with defined functional properties for single-cell genomics.

Heterotrophic bicarbonate assimilation is the main process of de novo organic carbon synthesis in hadal zone of the Hellenic Trench, the deepest part of Mediterranean Sea

Ammonium-oxidizing chemoautotrophic members of Thaumarchaea are proposed to be the key players in the assimilation of bicarbonate in the dark (ABD). However, this process may also involve heterotrophic metabolic pathways, such as fixation of carbon dioxide (CO2) via various anaplerotic reactions. We collected samples from the depth of 4900 m at the Matapan-Vavilov Deep (MVD) station (Hellenic Trench, Eastern Mediterranean) and used the multiphasic approach to study the ABD mediators in this deep-sea ecosystem. At this depth, our analysis indicated the occurrence of actively CO2-fixing heterotrophic microbial assemblages dominated by Gammaproteobacteria with virtually no Thaumarchaea present. [14C]-bicarbonate incorporation experiments combined with shotgun [14C]-proteomic analysis identified a series of proteins of gammaproteobacterial origin. More than quarter of them were closely related with Alteromonas macleodii ‘deep ecotype’ AltDE, the predominant organism in the microbial community of MVD. The present study demonstrated that in the aphotic/hadal zone of the Mediterranean Sea, the assimilation of bicarbonate is associated with both chemolithoauto- and heterotrophic ABD. In some deep-sea areas, the latter may predominantly contribute to the de novo synthesis of organic carbon which points at the important and yet underestimated role heterotrophic bacterial populations can play the in global carbon cycle/sink in the ocean interior.

Dynamics of metabolic activities and gene expression in the Roseobacter clade bacterium Phaeobacter sp. strain MED193 during growth with thiosulfate

Metagenomic analyses of surface seawater reveal that genes for sulfur oxidation are widespread in bacterioplankton communities. However, little is known about the metabolic processes used to exploit the energy potentially gained from inorganic sulfur oxidation in oxic seawater. We therefore studied the sox gene system containing Roseobacter clade isolate Phaeobacter sp. strain MED193 in acetate minimal medium with and without thiosulfate. The addition of thiosulfate enhanced the bacterial growth yields up to 40% in this strain. Concomitantly, soxB and soxY gene expression increased about 8-fold with thiosulfate and remained 11-fold higher than that in controls through stationary phase. At stationary phase, thiosulfate stimulated protein synthesis and anaplerotic CO2 fixation rates up to 5- and 35-fold, respectively. Several genes involved in anaplerotic CO2 fixation (i.e., pyruvate carboxylase, propionyl coenzyme A [CoA], and crotonyl-CoA carboxylase) were highly expressed during active growth, coinciding with high CO2 fixation rates. The high expression of key genes in the ethylmalonyl-CoA pathway suggests that this is an important pathway for the utilization of two-carbon compounds in Phaeobacter sp. MED193. Overall, our findings imply that Roseobacter clade bacteria carrying sox genes can use their lithotrophic potential to gain additional energy from sulfur oxidation for both increasing their growth capacity and improving their long-term survival.

Chemoautotrophic carbon fixation rates and active bacterial communities in intertidal marine sediments

Chemoautotrophy has been little studied in typical coastal marine sediments, but may be an important component of carbon recycling as intense anaerobic mineralization processes in these sediments lead to accumulation of high amounts of reduced compounds, such as sulfides and ammonium. We studied chemoautotrophy by measuring dark-fixation of ¹³C-bicarbonate into phospholipid derived fatty acid (PLFA) biomarkers at two coastal sediment sites with contrasting sulfur chemistry in the Eastern Scheldt estuary, the Netherlands. At one site where free sulfide accumulated in the pore water right to the top of the sediment, PLFA labeling was restricted to compounds typically found in sulfur and ammonium oxidizing bacteria. At the other site, with no detectable free sulfide in the pore water, a very different PLFA labeling pattern was found with high amounts of label in branched i- and a-PLFA besides the typical compounds for sulfur and ammonium oxidizing bacteria. This suggests that other types of chemoautotrophic bacteria were also active, most likely Deltaproteobacteria related to sulfate reducers. Maximum rates of chemoautotrophy were detected in first 1 to 2 centimeters of both sediments and chemosynthetic biomass production was high ranging from 3 to 36 mmol C m⁻² d⁻¹. Average dark carbon fixation to sediment oxygen uptake ratios were 0.22±0.07 mol C (mol O₂)⁻¹, which is in the range of the maximum growth yields reported for sulfur oxidizing bacteria indicating highly efficient growth. Chemoautotrophic biomass production was similar to carbon mineralization rates in the top of the free sulfide site, suggesting that chemoautotrophic bacteria could play a crucial role in the microbial food web and labeling in eukaryotic poly-unsaturated PLFA was indeed detectable. Our study shows that dark carbon fixation by chemoautotrophic bacteria is a major process in the carbon cycle of coastal sediments, and should therefore receive more attention in future studies on sediment biogeochemistry and microbial ecology.

Dark carbon fixation: an important process in lake sediments

Close to redox boundaries, dark carbon fixation by chemoautotrophic bacteria may be a large contributor to overall carbon fixation. Still, little is known about the relative importance of this process in lake systems, in spite the potentially high chemoautotrophic potential of lake sediments. We compared rates of dark carbon fixation, bacterial production and oxygen consumption in sediments from four Swedish boreal and seven tropical Brazilian lakes. Rates were highly variable and dark carbon fixation amounted up to 80% of the total heterotrophic bacterial production. The results indicate that non-photosynthetic carbon fixation can represent a substantial contribution to bacterial biomass production, especially in sediments with low organic matter content.

Contribution of microorganisms to non-extractable residue formation during biodegradation of ibuprofen in soil

Non-extractable residues (NER) formed during biodegradation of organic contaminants in soil are considered to be mainly composed of parent compounds or their primary metabolites with hazardous potential. However, in the case of biodegradable organic compounds, the soil NER may also contain microbial biomass components, for example fatty acids (FA) and amino acids (AA). After cell death, these biomolecules are subsequently incorporated into non-living soil organic matter (SOM) and are stabilised ultimately forming hardly extractable residues of biogenic origin. We investigated biodegradation of (13)C(6)-ibuprofen, in particular the metabolic incorporation of the (13)C-label into FA and AA and their fate in soil over 90 days. (13)C-FA and (13)C-AA amounts in the living microbial biomass fraction initially increased, then decreased over time and were continuously incorporated into the non-living SOM pool. The (13)C-FA in the non-living SOM remained stable from day 59 whereas the contents of (13)C-AA slightly increased until the end. After 90 days, nearly all NER were biogenic as they were made up almost completely by natural biomass compounds. The presented data demonstrated that the potential environmental risks related to the ibuprofen-derived NER are overestimated.

Interactions of nitrifying bacteria and heterotrophs: identification of a Micavibrio-like putative predator of Nitrospira spp

Chemolithoautotrophic nitrifying bacteria release soluble organic compounds, which can be substrates for heterotrophic microorganisms. The identities of these heterotrophs and the specificities of their interactions with nitrifiers are largely unknown. In this study, we incubated nitrifying activated sludge with (13)C-labeled bicarbonate and used stable isotope probing of 16S rRNA to monitor the flow of carbon from uncultured nitrifiers to heterotrophs. To facilitate the identification of heterotrophs, the abundant 16S rRNA molecules from nitrifiers were depleted by catalytic oligonucleotides containing locked nucleic acids (LNAzymes), which specifically cut the 16S rRNA of defined target organisms. Among the (13)C-labeled heterotrophs were organisms remotely related to Micavibrio, a microbial predator of Gram-negative bacteria. Fluorescence in situ hybridization revealed a close spatial association of these organisms with microcolonies of nitrite-oxidizing sublineage I Nitrospira in sludge flocs. The high specificity of this interaction was confirmed by confocal microscopy and a novel image analysis method to quantify the localization patterns of biofilm microorganisms in three-dimensional (3-D) space. Other isotope-labeled bacteria, which were affiliated with Thermomonas, colocalized less frequently with nitrifiers and thus were commensals or saprophytes rather than specific symbionts or predators. These results suggest that Nitrospira spp. are subject to bacterial predation, which may influence the abundance and diversity of these nitrite oxidizers and the stability of nitrification in engineered and natural ecosystems. In silico screening of published next-generation sequencing data sets revealed a broad environmental distribution of the uncultured Micavibrio-like lineage.

Radiation-induced impacts on the degradation of 2,4-D and the microbial population in soil microcosms

In a soil microcosm experiment, the influence of low-level (137)Cs and (90)Sr contamination on the degradation of (14)C-ring-labeled 2,4-dichlorophenoxyacetic acid (2,4-D) was studied. Two differently treated soils (one native soil and one soil sterilized and reinoculated with a biotic soil aliquot) were artificially contaminated with various concentrations of (137)Cs and (90)Sr as nitrate salts. The cumulative doses increased up to 4 Gy for 30 days of incubation in soil microcosms. Changes in microbial community structure were observed with help of the denaturing gradient gel electrophoresis (DGGE). A radiation-induced impact appeared only in the microcosms treated with 30 times the maximum contamination appearing in the exclusion zone around reactor 4 in Chernobyl. In contrast to the less contaminated soils, the mineralization of 2,4-D was delayed for 4 days before it recovered. Slight shifts in the microbial communities could be traced to radiation effects. However, other parameters had a major impact on mineralization and community structure. Thus the sterilization and reinoculation and, of course, application of the 2,4-D were predominantly reflected in the (14)CO(2) emissions and the DGGE gel patterns.

Ubiquitous dissolved inorganic carbon assimilation by marine bacteria in the Pacific Northwest coastal ocean as determined by stable isotope probing

In order to identify bacteria that assimilate dissolved inorganic carbon (DIC) in the northeast Pacific Ocean, stable isotope probing (SIP) experiments were conducted on water collected from 3 different sites off the Oregon and Washington coasts in May 2010, and one site off the Oregon Coast in September 2008 and March 2009. Samples were incubated in the dark with 2 mM (13)C-NaHCO(3), doubling the average concentration of DIC typically found in the ocean. Our results revealed a surprising diversity of marine bacteria actively assimilating DIC in the dark within the Pacific Northwest coastal waters, indicating that DIC fixation is relevant for the metabolism of different marine bacterial lineages, including putatively heterotrophic taxa. Furthermore, dark DIC-assimilating assemblages were widespread among diverse bacterial classes. Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes dominated the active DIC-assimilating communities across the samples. Actinobacteria, Betaproteobacteria, Deltaproteobacteria, Planctomycetes, and Verrucomicrobia were also implicated in DIC assimilation. Alteromonadales and Oceanospirillales contributed significantly to the DIC-assimilating Gammaproteobacteria within May 2010 clone libraries. 16S rRNA gene sequences related to the sulfur-oxidizing symbionts Arctic96BD-19 were observed in all active DIC assimilating clone libraries. Among the Alphaproteobacteria, clones related to the ubiquitous SAR11 clade were found actively assimilating DIC in all samples. Although not a dominant contributor to our active clone libraries, Betaproteobacteria, when identified, were predominantly comprised of Burkholderia. DIC-assimilating bacteria among Deltaproteobacteria included members of the SAR324 cluster. Our research suggests that DIC assimilation is ubiquitous among many bacterial groups in the coastal waters of the Pacific Northwest marine environment and may represent a significant metabolic process.

Effects of high CO2 concentrations on ecophysiologically different microorganisms

We investigated the effect of increasing CO(2) concentrations on the growth and viability of ecophysiologically different microorganisms to obtain information for a leakage scenario of CO(2) into shallow aquifers related to the capture and storage of CO(2) in deep geological sections. CO(2) concentrations in the gas phase varied between atmospheric conditions and 80% CO(2) for the aerobic strains Pseudomonas putida F1 and Bacillus subtilis 168 and up to 100% CO(2) for the anaerobic strains Thauera aromatica K172 and Desulfovibrio vulgaris Hildenborough. Increased CO(2) concentrations caused prolonged lag-phases, and reduced growth rates and cell yields; the extent of this effect was proportional to the CO(2) concentration. Additional experiments with increasing CO(2) concentrations and increasing pressure (1-5000 kPa) simulated situations occurring in deep CO(2) storage sites. Living cell numbers decreased significantly within 24 h at pressures ≥1000 kPa, demonstrating a severe lethal effect for the combination of high pressure and CO(2).

Cultivation-independent detection of autotrophic hydrogen-oxidizing bacteria by DNA stable-isotope probing

Knallgas bacteria are a physiologically defined group that is primarily studied using cultivation-dependent techniques. Given that current cultivation techniques fail to grow most bacteria, cultivation-independent techniques that selectively detect and identify knallgas bacteria will improve our ability to study their diversity and distribution. We used stable-isotope probing (SIP) to identify knallgas bacteria in rhizosphere soil of legumes and in a microbial mat from Obsidian Pool in Yellowstone National Park. When samples were incubated in the dark, incorporation of (13)CO(2) was H(2) dependent. SIP enabled the detection of knallgas bacteria that were not detected by cultivation, and the majority of bacteria identified in the rhizosphere soils were betaproteobacteria predominantly related to genera previously known to oxidize hydrogen. Bacteria in soil grew on hydrogen at concentrations as low as 100 ppm. A hydB homolog encoding a putative high-affinity NiFe hydrogenase was amplified from (13)C-labeled DNA from both vetch and clover rhizosphere soil. The results indicate that knallgas bacteria can be detected by SIP and populations that respond to different H(2) concentrations can be distinguished. The methods described here should be applicable to a variety of ecosystems and will enable the discovery of additional knallgas bacteria that are resistant to cultivation.

Assimilation of benzene carbon through multiple trophic levels traced by different stable isotope probing methodologies

The flow of benzene carbon along a food chain consisting of bacteria and eukaryotes, including larvae (Diptera: Chironomidae), was evaluated by total lipid fatty acids (TLFAs)-, amino acid- and protein-stable isotope probing (SIP). A coconut-fibre textile, colonized by a benzene-degrading biofilm, was sampled in a system established for the remediation of benzene, toluene, ethylbenzene and xylenes (BTEX)-polluted groundwater and incubated with (12)C- and [(13)C(6)]-benzene (>99 at.%) in a batch-scale experiment for 2-8 days. After 8 days, Chironomus sp. larvae were added to study carbon flow to higher trophic levels. Gas chromatography-combustion-isotope ratio monitoring mass spectrometry of TLFA showed increased isotope ratios in the (13)C-benzene-incubated biofilm. A higher (13)C-enrichment was observed in TLFAs, indicative of Gram-negative bacteria than for Gram-positive. Fatty acid indicators of eukaryotes showed significant (13)C-incorporation, but to a lower extent than bacterial indicators. Fatty acids extracted from larvae feeding on (13)C-biofilm reached an isotopic ratio of 1.55 at.%, illustrating that the larvae feed, to some extent, on labelled biomass. No (13)C-incorporation was detectable in larval proteins after their separation by sodium-dodecyl sulphate-polyacrylamide gel electrophoresis and analysis by nano-liquid-chromatography-mass spectrometry. The flow of benzene-derived carbon could be traced in a food web consisting of bacteria and eukaryotes.

Formation and fate of bound residues from microbial biomass during 2,4-D degradation in soil

During organic contaminant degradation in soil, bound or nonextractable residues (NER) are formed. Part of these residues may be biogenic, because degrading microorganisms assimilate carbon derived from the pollutant and mineralized CO(2) to form cellular components for example, [fatty acids (FA) and amino acids (AA)], which are subsequently stabilized within soil organic matter (SOM). We investigated the formation and fate of FA and AA from biodegradation of (13)C(6)-2,4-D in soil and the incorporation of the (13)C-label into living biomass via (13)CO(2) fixation. After 64 days of incubation, (13)C-AA in SOM indicated that 44% of the initially applied (13)C(6)-2,4-D equivalents had been converted to microbial biomass and finally to biogenic residues. The intermediate maximum of (13)C-FA in SOM indicated a 20% conversion of (13)C(6)-2,4-D to biomass, but (13)C-FA decreased to 50% of that value whereas (13)C-AA in the SOM remained stable. We provide the first evidence that nearly all bound residues from 2,4-D are biogenic, containing natural microbial residues stabilized in SOM. Because of biogenic residue formation, the potential risk of bound residues from readily metabolized xenobiotics in soils is highly overestimated. Hence, the formation of biogenic residues must be considered in general when performing mass balances of pollutant biodegradation in soils.