Meta-omics reveal Gallionellaceae and Rhodanobacter as interdependent key players for Fe(II) oxidation and nitrate reduction in the autotrophic enrichment culture KS

Nitrate reduction coupled to iron(II) oxidation (NRFO) has been recognized as an environmentally important microbial process in many freshwater ecosystems. However, well-characterized examples of autotrophic nitrate-reducing iron(II)-oxidizing bacteria are rare and their pathway of electron transfer as well as their interaction with flanking community members remain largely unknown. Here, we applied meta-omics (i.e., metagenomics, metatranscriptomics and metaproteomics) to the nitrate-reducing iron(II)-oxidizing enrichment culture KS, growing under autotrophic compared to heterotrophic conditions, and originating from a freshwater sediment. We constructed four metagenome-assembled genomes with an estimated completeness of ≥95%, including the key players of NRFO in culture KS, identified as Gallionellaceae sp. and Rhodanobacter sp. The presence of Gallionellaceae sp. and Rhodanobacter sp. transcripts and proteins likely involved in iron(II) oxidation (e.g., mtoAB, cyc2, mofA), denitrification (e.g., napGHI) and oxidative phosphorylation (e.g., respiratory chain complexes I-V), along with Gallionellaceae sp. transcripts and proteins for carbon fixation (e.g., rbcL) were detected. Overall, our results indicate that in culture KS, the Gallionellaceae sp. and Rhodanobacter sp. are interdependent: while Gallionellaceae sp. fixes CO2 and provides organic compounds for Rhodanobacter sp., Rhodanobacter sp. likely detoxifies NO through NO reduction and completes denitrification, which cannot be done by Gallionellaceae sp. alone. Additionally, the transcripts and partial proteins of cbb3- and aa3- type cytochrome c suggest the possibility for a microaerophilic lifestyle of the Gallionellaceae sp., yet culture KS grows under anoxic conditions. Our findings demonstrate that autotrophic NRFO is performed through cooperation among denitrifying and iron(II)-oxidizing bacteria, which might resemble microbial interactions in freshwater environments. Importance Nitrate-reducing iron(II)-oxidizing bacteria are widespread in the environment, contribute to nitrate removal, and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing iron(II)-oxidizing bacteria is rarely investigated and not fully understood. The most prominent model system for this type of studies is the enrichment culture KS. To gain insights into the metabolism of nitrate reduction coupled to iron(II) oxidation in the absence of organic carbon and oxygen, we performed metagenomic, metatranscriptomic and metaproteomic analyses of culture KS, and identified Gallionellaceae sp. and Rhodanobacter sp. as interdependent key iron(II)-oxidizers in culture KS. Our work demonstrates that autotrophic nitrate reduction coupled to iron(II) oxidation is not performed by an individual strain but a cooperation of at least two members of the bacterial community in culture KS. These findings serve as foundation for our understanding of nitrate-reducing iron(II)-oxidizing bacteria in the environment.

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A Novel Enrichment Culture Highlights Core Features of Microbial Networks Contributing to Autotrophic Fe(II) Oxidation Coupled to Nitrate Reduction

Microbial Physiology ◽

10.1159/000517083 ◽

2021 ◽

pp. 1-16

Author(s):

Yu-Ming Huang ◽

Daniel Straub ◽

Andreas Kappler ◽

Nicole Smith ◽

Nia Blackwell ◽

...

Keyword(s):

Relative Abundance ◽

Nitrate Reduction ◽

Carbon Fixation ◽

Enrichment Culture ◽

Amplicon Sequencing ◽

Microbial Interactions ◽

Rrna Gene ◽

Metal Oxidation ◽

Core Features

Fe(II) oxidation coupled to nitrate reduction (NRFO) has been described for many environments. Yet very few autotrophic microorganisms catalysing NRFO have been cultivated and their diversity, as well as their mechanisms for NRFO in situ remain unclear. A novel autotrophic NRFO enrichment culture, named culture BP, was obtained from freshwater sediment. After more than 20 transfers, culture BP oxidized 8.22 mM of Fe(II) and reduced 2.42 mM of nitrate within 6.5 days under autotrophic conditions. We applied metagenomic, metatranscriptomic, and metaproteomic analyses to culture BP to identify the microorganisms involved in autotrophic NRFO and to unravel their metabolism. Overall, twelve metagenome-assembled genomes (MAGs) were constructed, including a dominant Gallionellaceae sp. MAG (≥71% relative abundance). Genes and transcripts associated with potential Fe(II) oxidizers in culture BP, identified as a Gallionellaceae sp., Noviherbaspirillum sp., and Thiobacillus sp., were likely involved in metal oxidation (e.g., cyc2, mtoA), denitrification (e.g., nirK/S, norBC), carbon fixation (e.g., rbcL), and oxidative phosphorylation. The putative Fe(II)-oxidizing protein Cyc2 was detected for the Gallionellaceae sp. Overall, a complex network of microbial interactions among several Fe(II) oxidizers and denitrifiers was deciphered in culture BP that might resemble NRFO mechanisms in situ. Furthermore, 16S rRNA gene amplicon sequencing from environmental samples revealed 36 distinct Gallionellaceae taxa, including the key player of NRFO from culture BP (approx. 0.13% relative abundance in situ). Since several of these in situ-detected Gallionellaceae taxa were closely related to the key player in culture BP, this suggests that the diversity of organisms contributing to NRFO might be higher than currently known.

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Data on effects of rotenone on calcium retention capacity, respiration and activities of respiratory chain complexes I and II in isolated rat brain mitochondria

Data in Brief ◽

10.1016/j.dib.2017.06.052 ◽

2017 ◽

Vol 13 ◽

pp. 707-712 ◽

Cited By ~ 2

Author(s):

Evelina Rekuviene ◽

Laima Ivanoviene ◽

Vilmante Borutaite ◽

Ramune Morkuniene

Keyword(s):

Rat Brain ◽

Respiratory Chain ◽

Brain Mitochondria ◽

Respiratory Chain Complexes ◽

Retention Capacity ◽

Calcium Retention ◽

Rat Brain Mitochondria ◽

Chain Complexes ◽

Calcium Retention Capacity ◽

Isolated Rat

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Expression of Mitochondrial Respiratory Chain Complexes in the Vaginal Wall in Postmenopausal Women with Pelvic Organ Prolapse

Gynecologic and Obstetric Investigation ◽

10.1159/000480236 ◽

2017 ◽

Vol 83 (5) ◽

pp. 487-492 ◽

Cited By ~ 1

Author(s):

Ivana Alujević Jakus ◽

Dora Jakus ◽

Jasna Marinović ◽

Marija Ćavar ◽

Ivana Banić ◽

...

Keyword(s):

Pelvic Organ Prolapse ◽

Postmenopausal Women ◽

Respiratory Chain ◽

Mitochondrial Respiratory Chain ◽

Pelvic Organ ◽

Vaginal Wall ◽

Respiratory Chain Complexes ◽

Chain Complexes ◽

Mitochondrial Respiratory

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Decreased activities of mitochondrial respiratory chain complexes in non-mitochondrial respiratory chain diseases

Developmental Medicine & Child Neurology ◽

10.1017/s0012162206000284 ◽

2006 ◽

Vol 48 (2) ◽

pp. 132-136 ◽

Cited By ~ 30

Author(s):

Joannie Hui MBBS ◽

Denise M Kirby ◽

David R Thorburn ◽

A vihu Boneh

Keyword(s):

Respiratory Chain ◽

Mitochondrial Respiratory Chain ◽

Respiratory Chain Complexes ◽

Chain Complexes ◽

Mitochondrial Respiratory

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Assembly factors monitor sequential hemylation of cytochrome b to regulate mitochondrial translation

The Journal of Cell Biology ◽

10.1083/jcb.201401009 ◽

2014 ◽

Vol 205 (4) ◽

pp. 511-524 ◽

Cited By ~ 40

Author(s):

Markus Hildenbeutel ◽

Eric L. Hegg ◽

Katharina Stephan ◽

Steffi Gruschke ◽

Brigitte Meunier ◽

...

Keyword(s):

Electron Transport ◽

Cytochrome B ◽

Mitochondrial Respiratory Chain ◽

Complex Iii ◽

Mitochondrial Translation ◽

Respiratory Chain Complexes ◽

Mitochondrial Inner Membrane ◽

Sequence Of Events ◽

Chain Complexes ◽

Assembly Factors

Mitochondrial respiratory chain complexes convert chemical energy into a membrane potential by connecting electron transport with charge separation. Electron transport relies on redox cofactors that occupy strategic positions in the complexes. How these redox cofactors are assembled into the complexes is not known. Cytochrome b, a central catalytic subunit of complex III, contains two heme bs. Here, we unravel the sequence of events in the mitochondrial inner membrane by which cytochrome b is hemylated. Heme incorporation occurs in a strict sequential process that involves interactions of the newly synthesized cytochrome b with assembly factors and structural complex III subunits. These interactions are functionally connected to cofactor acquisition that triggers the progression of cytochrome b through successive assembly intermediates. Failure to hemylate cytochrome b sequesters the Cbp3–Cbp6 complex in early assembly intermediates, thereby causing a reduction in cytochrome b synthesis via a feedback loop that senses hemylation of cytochrome b.

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Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations

mSystems ◽

10.1128/msystems.01196-20 ◽

2021 ◽

Vol 6 (3) ◽

Author(s):

Sarahi L. Garcia ◽

Maliheh Mehrshad ◽

Moritz Buck ◽

Jackson M. Tsuji ◽

Josh D. Neufeld ◽

...

Keyword(s):

Carbon Fixation ◽

Carbon Sources ◽

Natural Populations ◽

Freshwater Ecosystems ◽

Electron Donors ◽

Functional Ecology ◽

Lake Ecosystems ◽

Tropical Regions ◽

Metabolic Versatility ◽

Globally Distributed

ABSTRACT Photosynthetic bacteria from the class Chlorobia (formerly phylum Chlorobi) sustain carbon fixation in anoxic water columns. They harvest light at extremely low intensities and use various inorganic electron donors to fix carbon dioxide into biomass. Until now, most information on the functional ecology and local adaptations of Chlorobia members came from isolates and merely 26 sequenced genomes that may not adequately represent natural populations. To address these limitations, we analyzed global metagenomes to profile planktonic Chlorobia cells from the oxyclines of 42 freshwater bodies, spanning subarctic to tropical regions and encompassing all four seasons. We assembled and compiled over 500 genomes, including metagenome-assembled genomes (MAGs), single-amplified genomes (SAGs), and reference genomes from cultures, clustering them into 71 metagenomic operational taxonomic units (mOTUs or “species”). Of the 71 mOTUs, 57 were classified within the genus Chlorobium, and these mOTUs represented up to ∼60% of the microbial communities in the sampled anoxic waters. Several Chlorobium-associated mOTUs were globally distributed, whereas others were endemic to individual lakes. Although most clades encoded the ability to oxidize hydrogen, many lacked genes for the oxidation of specific sulfur and iron substrates. Surprisingly, one globally distributed Scandinavian clade encoded the ability to oxidize hydrogen, sulfur, and iron, suggesting that metabolic versatility facilitated such widespread colonization. Overall, these findings provide new insight into the biogeography of the Chlorobia and the metabolic traits that facilitate niche specialization within lake ecosystems. IMPORTANCE The reconstruction of genomes from metagenomes has helped explore the ecology and evolution of environmental microbiota. We applied this approach to 274 metagenomes collected from diverse freshwater habitats that spanned oxic and anoxic zones, sampling seasons, and latitudes. We demonstrate widespread and abundant distributions of planktonic Chlorobia-associated bacteria in hypolimnetic waters of stratified freshwater ecosystems and show they vary in their capacities to use different electron donors. Having photoautotrophic potential, these Chlorobia members could serve as carbon sources that support metalimnetic and hypolimnetic food webs.

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Relationships between the activity of respiratory-chain complexes in pre- (biopsy) or post-slaughter muscle samples and feed efficiency in random-bred Ghezel lambs

Animal Production Science ◽

10.1071/an15184 ◽

2017 ◽

Vol 57 (8) ◽

pp. 1674

Author(s):

M. J. Zamiri ◽

R. Mehrabi ◽

G. R. Kavoosi ◽

H. Rajaei Sharifabadi

Keyword(s):

Respiratory Chain ◽

Feed Intake ◽

Enzyme Activities ◽

Feed Efficiency ◽

Average Daily Gain ◽

Chain Complex ◽

Respiratory Chain Complex ◽

Respiratory Chain Complexes ◽

Chain Complexes ◽

Daily Gain

The present study was conducted to determine the relationship between the activity of mitochondrial respiratory chain complexes in pre- and post-slaughter muscle samples and residual feed intake (RFI) in Ghezel male lambs born as a result of random mating. The study was based on the hypothesis that random-bred lambs with lower feed (or higher) RFI have lower (or higher) respiratory chain-complex activity in muscle samples. Lambs (n = 30) were fed a diet consisting of 70% concentrate and 30% alfalfa hay during a 70-day period. Individual feed intake and average daily gain were recorded to calculate the RFI, feed-conversion ratio (FCR) and adjusted FCR (aFCR). On the basis of these calculations, the lambs were classified into low and high groups for RFI, with FCR and aFCR (n = 22) being one standard deviation above or below the means; this was corroborated by Student’s t-test (P < 0.01). At the end of the experiment, a 10-g biopsy sample was taken from the posterior side of the left femoral biceps. After 24 h, the lambs were slaughtered, and a sample from the posterior side of the right femoral biceps was dissected for determination of mitochondrial protein and respiratory chain-complex activities (Complexes I–V). The RFI was not correlated with the metabolic bodyweight and average daily gain, but was positively correlated (r = 0.56) with the average daily feed intake (P < 0.01); mean daily feed intake in the low-RFI group was 200 g less than that in the high-RFI group. The FCR and aFCR were not significantly (P > 0.05) correlated with average daily feed intake (r = 0.39 and r = 0.36 respectively), but showed a negative correlation (P < 0.01) with average daily gain (r = –0.73 and r = –0.76 respectively). Although very high negative correlations were recorded between the activities of all five respiratory-chain complexes and RFI in muscle samples obtained before (–0.91 to –0.97) and after (–0.92 to –0.97) slaughter, Complexes I and V showed small negative correlations (–0.40) with FCR or aFCR (P < 0.05). Enzyme activities of the respiratory-chain Complexes I, III and V were not significantly different between the pre- and post-slaughter biopsy samples; however, the enzyme activities of respiratory-chain Complexes II and IV were slightly higher in post-slaughter samples (P < 0.01). These results suggested that it may be possible to use the enzymatic activity of respiratory-chain complexes in muscle biopsy samples for screening of lambs for RFI, providing a useful procedure for genetic selection of lambs for this component of feed efficiency. These encouraging results need to be verified in further experiments using other sheep breeds and a larger number of lambs.

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