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"Autotrophic bacteria"
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Nitrogen application increases soil microbial carbon fixation and maize productivity on the semiarid Loess Plateau
Background and aimsSoil autotrophic microorganisms and plant primary production play crucial roles in soil carbon (C) cycling. However, the information remains limited to whether and how nitrogen (N) application influences the contribution of soil microbial C fixation to the soil organic C (SOC) pool.MethodsWe investigated the effects of soil autotrophic bacterial communities on SOC storage and maize yield. A field experiment was conducted with four application rates of urea on the semiarid Loess Plateau, N application at 0 kg ha− 1 (N0), 100 kg ha− 1 (N1), 200 kg ha− 1 (N2), and 300 kg ha− 1 (N3), respectively.ResultsOur results showed that SOC storage and maize yield were significantly increased by N application, but no significant SOC storage difference between N2 and N3 treatments, no further yield increase beyond 200 N kg ha− 1 application was observed. N application significantly impacted soil Calvin-Benson-Bassham (CBB) (cbbL) gene-carrying bacterial communities via changing soil pH, nitrate N, and soil water content. The diversity of soil autotrophic bacterial communities decreased with increasing rate of N application. We detected a high abundance of the autotrophic bacterial dominant genera Xanthobacter, Bradyrhizobium, Aminobacter, and Nitrosospira. The co-occurrence network of autotrophic bacteria contained four distinct modules. Structural equation modeling further indicated that the autotrophic bacterial communities had positive relationships with SOC storage and maize yield.ConclusionsTaken together, our results highlighted that N application stimulated the activity of soil autotrophic bacterial communities, contributing to an increase in SOC. The increase of SOC under N fertilization can stabilize soil fertility for maize production.
Journal Article
Evolution of primary producers in the sea
This text reference examines how photosynthesis evolved on Earth and how phytoplankton evolved through time - ultimately to permit the evolution of complex life, including human beings. The first of its kind, this book provides thorough coverage of key topics, with contributions by leading experts in biophysics, evolutionary biology, micropaleontology, marine ecology, and biogeochemistry.This exciting new book is of interest not only to students and researchers in marine science, but also to evolutionary biologists and ecologists interested in understanding the origins and diversification of life. Primary Producers of the Sea offers these students and researchers an understanding of the molecular evolution, phylogeny, fossil record, and environmental processes that collectively permits us to comprehend the rise of phytoplankton and their impact on Earth's ecology and biogeochemistry. It is certain to become the first and best word on this exhilarating topic. * Discusses the evolution of phytoplankton in the world's oceans as the first living organisms and the first and basic producers in the earths food chain* Includes the latest developments in the evolution and ecology of marine phytoplankton specifically with additional information on marine ecosystems and biogeochemical cycles* The only book to consider of the evolution of phytoplankton and its role in molecular evolution, biogeochemistry, paleontology, and oceanographic aspects * Written at a level suitable for related reading use in courses on the Evolution of the Biosphere, Ecological and Biological oceanography and marine biology, and Biodiversity
eBook
Continuous-flow membrane bioreactor enhances enrichment and culture of autotrophic nitrifying bacteria by removing extracellular free organic carbon
An activated sludge system can be inoculated with enriched nitrifying bacteria to enhance NH
4
+
-N removal, or enriched nitrifying bacteria can be added directly to a river to remove NH
4
+
-N. However, the enrichment culture is still generally inefficient and the technical bottleneck has not been clarified. Previous studies have shown that extracellular free organic carbon (EFOC) inhibits the growth of some autotrophic bacteria, and separating EFOC during culture with a membrane bioreactor (MBR) promotes the continuous growth of autotrophic bacteria and CO
2
fixation. However, whether a membrane bioreactor can also be used to enrich and culture autotrophic nitrifying bacteria by separating EFOC has not been verified. In this study, an MBR was constructed to separate EFOC during the culture of nitrifying bacteria in activated sludge to confirm that the MBR better enriches and cultures nitrifying bacteria than a sequencing batch reactor (SBR). Our results showed that after culture for 34 days, the rate of NH
4
+
-N removal and the nitrification rate by nitrifying bacteria in the MBR were 2.20-fold and 1.42-fold higher than in the SBR, respectively. The abundance of
Nitrospira
in the MBR was also 7.23-fold greater than in the SBR at the end of the experimental period. After 34 days, the average concentration of EFOC and the average EFOC/bacterial organic carbon ratio in the MBR were only 53% and 37% of those in the SBR, respectively. A correlation analysis suggested that the timely removal by the MBR of the EFOC generated during the culture process may be an important factor in promoting the growth of autotrophic nitrifying bacteria. The possible mechanism by which the MBR separates EFOC to the growth of promote autotrophic nitrifying bacteria is discussed from the perspective of the inhibitory effect of EFOC on
cbb
gene transcription. Our experimental results suggest a new approach to enhancing the enrichment of autotrophic nitrifying bacteria and extending the application of MBRs.
Journal Article
Soil Carbon-Fixation Rates and Associated Bacterial Diversity and Abundance in Three Natural Ecosystems
CO₂ assimilation by autotrophic microbes is an important process in soil carbon cycling, and our understanding of the community composition of autotrophs in natural soils and their role in carbon sequestration of these soils is still limited. Here, we investigated the autotrophic C incorporation in soils from three natural ecosystems, i.e., wetland (WL), grassland (GR), and forest (FO) based on the incorporation of labeled C into the microbial biomass. Microbial assimilation of ¹⁴C (¹⁴C-MBC) differed among the soils from three ecosystems, accounting for 14.2–20.2% of ¹⁴C-labeled soil organic carbon (¹⁴C-SOC). We observed a positive correlation between the cbbL (ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) large-subunit gene) abundance, ¹⁴C-SOC level, and ¹⁴C-MBC concentration confirming the role of autotrophic bacteria in soil carbon sequestration. Distinct cbbL-bearing bacterial communities were present in each soil type; form IA and form IC RubisCO-bearing bacteria were most abundant in WL, followed by GR soils, with sequences from FO soils exclusively derived from the form IC clade. Phylogenetically, the diversity of CO₂-fixing autotrophs and CO oxidizers differed significantly with soil type, whereas cbbL-bearing bacterial communities were similar when assessed using coxL. We demonstrate that local edaphic factors such as pH and salinity affect the C-fixation rate as well as cbbL and coxL gene abundance and diversity. Such insights into the effect of soil type on the autotrophic bacterial capacity and subsequent carbon cycling of natural ecosystems will provide information to enhance the sustainable management of these important natural ecosystems.
Journal Article
Cell-free prototyping enables implementation of optimized reverse β-oxidation pathways in heterotrophic and autotrophic bacteria
Carbon-negative synthesis of biochemical products has the potential to mitigate global CO
2
emissions. An attractive route to do this is the reverse β-oxidation (r-BOX) pathway coupled to the Wood-Ljungdahl pathway. Here, we optimize and implement r-BOX for the synthesis of C4-C6 acids and alcohols. With a high-throughput in vitro prototyping workflow, we screen 762 unique pathway combinations using cell-free extracts tailored for r-BOX to identify enzyme sets for enhanced product selectivity. Implementation of these pathways into
Escherichia coli
generates designer strains for the selective production of butanoic acid (4.9 ± 0.1 gL
−1
), as well as hexanoic acid (3.06 ± 0.03 gL
−1
) and 1-hexanol (1.0 ± 0.1 gL
−1
) at the best performance reported to date in this bacterium. We also generate
Clostridium autoethanogenum
strains able to produce 1-hexanol from syngas, achieving a titer of 0.26 gL
−1
in a 1.5 L continuous fermentation. Our strategy enables optimization of r-BOX derived products for biomanufacturing and industrial biotechnology.
An attractive route for carbon-negative synthesis of biochemical products is the reverse β-oxidation pathway coupled to the Wood-Ljungdahl pathway. Here the authors use a high-throughput in vitro prototyping workflow to screen 762 unique pathway combinations using cell-free extracts tailored for r-BOX to identify enzyme sets for enhanced product selectivity.
Journal Article
Membrane-anchored HDCR nanowires drive hydrogen-powered CO2 fixation
Filamentous enzymes have been found in all domains of life, but the advantage of filamentation is often elusive
1
. Some anaerobic, autotrophic bacteria have an unusual filamentous enzyme for CO
2
fixation—hydrogen-dependent CO
2
reductase (HDCR)
2
,
3
—which directly converts H
2
and CO
2
into formic acid. HDCR reduces CO
2
with a higher activity than any other known biological or chemical catalyst
4
,
5
, and it has therefore gained considerable interest in two areas of global relevance: hydrogen storage and combating climate change by capturing atmospheric CO
2
. However, the mechanistic basis of the high catalytic turnover rate of HDCR has remained unknown. Here we use cryo-electron microscopy to reveal the structure of a short HDCR filament from the acetogenic bacterium
Thermoanaerobacter kivui
. The minimum repeating unit is a hexamer that consists of a formate dehydrogenase (FdhF) and two hydrogenases (HydA2) bound around a central core of hydrogenase Fe-S subunits, one HycB3 and two HycB4. These small bacterial polyferredoxin-like proteins oligomerize through their C-terminal helices to form the backbone of the filament. By combining structure-directed mutagenesis with enzymatic analysis, we show that filamentation and rapid electron transfer through the filament enhance the activity of HDCR. To investigate the structure of HDCR in situ, we imaged
T. kivui
cells with cryo-electron tomography and found that HDCR filaments bundle into large ring-shaped superstructures attached to the plasma membrane. This supramolecular organization may further enhance the stability and connectivity of HDCR to form a specialized metabolic subcompartment within the cell.
The cryo-electron microscopy structure of the filamentous hydrogen-dependent CO
2
reductase (HDCR) enzyme from
Thermoanaerobacter kivui
, together with enzymatic analysis and in situ cryo-electron tomography, provides insight into the high catalytic activity of HDCR.
Journal Article
Form III RubisCO-mediated transaldolase variant of the Calvin cycle in a chemolithoautotrophic bacterium
The Calvin–Benson–Bassham (CBB) cycle assimilates CO₂ for the primary production of organic matter in all plants and algae, as well as in some autotrophic bacteria. The key enzyme of the CBB cycle, ribulose-bisphosphate carboxylase/oxygenase (RubisCO), is a main determinant of de novo organic matter production on Earth. Of the three carboxylating forms of RubisCO, forms I and II participate in autotrophy, and form III so far has been associated only with nucleotide and nucleoside metabolism. Here, we report that form III RubisCO functions in the CBB cycle in the thermophilic chemolithoautotrophic bacterium Thermodesulfobium acidiphilum, a phylum-level lineage representative. We further show that autotrophic CO₂ fixation in T. acidiphilum is accomplished via the transaldolase variant of the CBB cycle, which has not been previously demonstrated experimentally and has been considered unlikely to occur. Thus, this work reveals a distinct form of the key pathway of CO₂ fixation.
Journal Article
Rubisco forms a lattice inside alpha-carboxysomes
Despite the importance of microcompartments in prokaryotic biology and bioengineering, structural heterogeneity has prevented a complete understanding of their architecture, ultrastructure, and spatial organization. Here, we employ cryo-electron tomography to image α-carboxysomes, a pseudo-icosahedral microcompartment responsible for carbon fixation. We have solved a high-resolution subtomogram average of the Rubisco cargo inside the carboxysome, and determined the arrangement of the enzyme. We find that the
H. neapolitanus
Rubisco polymerizes in vivo, mediated by the small Rubisco subunit. These fibrils can further pack to form a lattice with six-fold pseudo-symmetry. This arrangement preserves freedom of motion and accessibility around the Rubisco active site and the binding sites for two other carboxysome proteins, CsoSCA (a carbonic anhydrase) and the disordered CsoS2, even at Rubisco concentrations exceeding 800 μM. This characterization of Rubisco cargo inside the α-carboxysome provides insight into the balance between order and disorder in microcompartment organization.
Many autotrophic bacteria rely on Rubisco for carbon dioxide fixation. Here the authors report the position, orientation, and structure of Rubisco within alpha-carboxysomes; showing how it polymerizes and can form a lattice inside this compartment.
Journal Article
Autotrophic ammonia oxidation by soil thaumarchaea
Nitrification plays a central role in the global nitrogen cycle and is responsible for significant losses of nitrogen fertilizer, atmospheric pollution by the greenhouse gas nitrous oxide, and nitrate pollution of groundwaters. Ammonia oxidation, the first step in nitrification, was thought to be performed by autotrophic bacteria until the recent discovery of archaeal ammonia oxidizers. Autotrophic archaeal ammonia oxidizers have been cultivated from marine and thermal spring environments, but the relative importance of bacteria and archaea in soil nitrification is unclear and it is believed that soil archaeal ammonia oxidizers may use organic carbon, rather than growing autotrophically. In this soil microcosm study, stable isotope probing was used to demonstrate incorporation of ¹³C-enriched carbon dioxide into the genomes of thaumarchaea possessing two functional genes: amoA, encoding a subunit of ammonia monooxygenase that catalyses the first step in ammonia oxidation; and hcd, a key gene in the autotrophic 3-hydroxypropionate/4-hydroxybutyrate cycle, which has been found so far only in archaea. Nitrification was accompanied by increases in archaeal amoA gene abundance and changes in amoA gene diversity, but no change was observed in bacterial amoA genes. Archaeal, but not bacterial, amoA genes were also detected in ¹³C-labeled DNA, demonstrating inorganic CO₂ fixation by archaeal, but not bacterial, ammonia oxidizers. Autotrophic archaeal ammonia oxidation was further supported by coordinate increases in amoA and hcd gene abundance in ¹³C-labeled DNA. The results therefore provide direct evidence for a role for archaea in soil ammonia oxidation and demonstrate autotrophic growth of ammonia oxidizing archaea in soil.
Journal Article