Anaerobic oxidation of ammonium (anammox) is recognized as an important process in the marine nitrogen cycle yet nothing is known about the distribution, diversity and activity of anammox bacteria in ...the terrestrial realm. In this study, we report on the detection of anammox sequences of Candidatus 'Brocadia', 'Kuenenia', 'Scalindua' and 'Jettenia' in marshes, lakeshores, a contaminated porous aquifer, permafrost soil, agricultural soil and in samples associated with nitrophilic or nitrogen-fixing plants. This suggests a higher diversity of anammox bacteria in terrestrial than in marine ecosystems and could be a consequence of the larger variety of suitable niches in soils. Anammox bacteria were not ubiquitously present but were only detected in certain soil types and at particular depths, thus reflecting specific ecological requirements. As opposed to marine water column habitats where Candidatus 'Scalindua' dominates anammox guilds, 'Kuenenia' and 'Brocadia' appear to be the most common representatives in terrestrial environments.
The scarcity of non-renewable resources such as soils and fertilizers and the consequences of climate change can dramatically influence the food security of future generations. Mutualistic root ...microorganisms such as plant growth-promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF) can improve plant fitness. We tested the growth response of wheat (Triticum aestivum L.), rice (Oriza sativa L.) and black gram (Vigna mungo L., Hepper) to an inoculation of AMF and PGPR alone or in combination over two years at seven locations in a region extending from the Himalayan foothills to the Indo-Gangetic plain. The AMF applied consisted of a consortium of different strains, the PGPR of two fluorescent Pseudomonas strains (Pseudomonas jessenii, R62; Pseudomonas synxantha, R81), derived from wheat rhizosphere from one test region. We found that dual inoculation of wheat with PGPR and AMF increased grain yield by 41% as compared to un-inoculated controls. Yield responses to the inoculants were highest at locations with previously low yields. AMF or PGPR alone augmented wheat grain yield by 29% and 31%, respectively. The bio-inoculants were effective both at Zero and at farmers’ practice fertilization level (70 kg N ha−1, 11 kg P ha−1 in mineral form to wheat crop). Also raw protein (nitrogen × 5.7) and mineral nutrient concentration of wheat grains (phosphorus, potassium, copper, iron, zinc, manganese) were higher after inoculation (+6% to +53%). Phosphorus use efficiency of wheat grains kg P grain kg−1 P fertilizer was increased by 95%. AMF and PGPR application also improved soil quality as indicated by increased soil enzyme activities of alkaline and acid phosphatase, urease and dehydrogenase. Effects on rice and black gram yields were far less pronounced over two cropping seasons, suggesting that AMF and PGPR isolated from the target crop were more efficient. We conclude that mutualistic root microorganisms have a high potential for contributing to food security and for improving nutrition status in southern countries, while safeguarding natural resources such as P stocks.
► Crop response to bio-inoculants isolated from wheat was highest in wheat (+41%). ► Consortia of AMF and PGPR were more effective than single inoculants. ► Bio-inoculants were most effective at sites with previously low yield. ► Also soil enzymes and mineral nutrient concentration of wheat grains were increased. ► Inoculants have a high potential to increase food security and resource use efficiency.
Precambrian Banded Iron Formation (BIF) deposition was conventionally attributed to the precipitation of iron-oxides resulting from the abiotic reaction of ferrous iron (Fe(II)) with ...photosynthetically produced oxygen. Earliest traces of oxygen date from 2.7 Ga, thus raising questions as to what may have caused BIF precipitation before oxygenic photosynthesis evolved. The discovery of anoxygenic phototrophic bacteria thriving through the oxidation of Fe(II) has provided support for a biological origin for some BIFs, but despite reports suggesting that anoxygenic phototrophs may oxidize Fe(II) in the environment, a model ecosystem of an ancient ocean where they are demonstrably active was lacking. Here we show that anoxygenic phototrophic bacteria contribute to Fe(II) oxidation in the water column of the ferruginous sulfate-poor, meromictic lake La Cruz (Spain). We observed in-situ photoferrotrophic activity through stimulation of phototrophic carbon uptake in the presence of Fe(II), and determined light-dependent Fe(II)-oxidation by the natural chemocline microbiota. Moreover, a photoferrotrophic bacterium most closely related to Chlorobium ferrooxidans was enriched from the ferruginous water column. Our study for the first time demonstrates a direct link between anoxygenic photoferrotrophy and the anoxic precipitation of Fe(III)-oxides in a ferruginous water column, providing a plausible mechanism for the bacterial origin of BIFs before the advent of free oxygen. However, photoferrotrophs represent only a minor fraction of the anoxygenic phototrophic community with the majority apparently thriving by sulfur cycling, despite the very low sulfur content in the ferruginous chemocline of Lake La Cruz.
ABSTRACT
White lupins (Lupinus albus L.) respond to phosphate deficiency by producing special root structures called cluster roots. These cluster roots secrete large amounts of carboxylates into the ...rhizosphere, mostly citrate and malate, which act as phosphate solubilizers and enable the plant to grow in soils with sparingly available phosphate. The success and efficiency of such a P‐acquisition strategy strongly depends on the persistence and stability of the carboxylates in the soil, a parameter that is influenced to a large extent by biodegradation through rhizosphere bacteria and fungi. In this study, we show that white lupin roots use several mechanisms to reduce microbial growth. The abundance of bacteria associated with cluster roots was decreased at the mature state of the cluster roots, where a burst of organic acid excretion and a drastic pH decrease is observed. Excretion of phenolic compounds, mainly isoflavonoids, induced fungal sporulation, indicating that vegetative growth, and thus potential citrate consumption, is reduced. In addition, the activity of two antifungal cell wall‐degrading enzymes, chitinase and glucanase, were highest at the stage preceding the citrate excretion. Therefore, our results suggest that white lupin has developed a complex strategy to reduce microbial degradation of the phosphate‐solubilizing agents.
In this study, Bauxsol pellets packed in PVC columns were used to remove nutrients and trace-metals from municipal wastewater during a 6 months field trial. Bauxsol pellet columns showed a high ...phosphate removal rate via precipitation of PO4 3- with Ca2+ and Mg2+ ions: at 90% in the 1st month; at 80% from the second to fifth months; and at 60% in the sixth month. Pellet bound total phosphorus and Colwell phosphorus were 7.3 g/kg and 2 g/kg and are about 20 times the concentrations found in most fertile soils. Trace-metals in effluents were bound, probably irreversibly under the columns’ environmental conditions, to the Bauxsol minerals that have high surface area to volume ratios and high charge to mass ratios. Experimental results showed a complex nitrogen cycle operating within the Bauxsol pellet columns including anoxic nitrification, denitrification, and anammox processes. Although a transient pH spike, associated with the release of unreacted CaO from the cement binder used in the pellets, was observed, this may be readily corrected through post-treatment pH adjustment. Hence, the geochemistry of Bauxsol pellets can effectively remove and bind nutrients and trace-metals during wastewater treatment, and further research may show that saturated spent pellets can be used as fertilizer.
The rhizosphere of
Trifolium repens and
Lolium perenne was divided into three fractions: the bulk soil; the soil adhering to the roots; and the washed roots (rhizoplane and endorhizosphere). After ...isolation and purification of DNA from these fractions, 16S rDNA was amplified by PCR and cloned to obtain a collection of 16S rRNA genes representative of the bacterial communities of these three fractions. The cloned 16S rRNA genes were then partially sequenced and analysed by a molecular phylogenetic approach. Our data show a high diversity in the bulk soil, which is dominated by clones related to Gram-positive,
Cytophaga–Flexibacter–Bacteroides, Proteobacteria, and
Holophaga–Acidobacterium groups. The ubiquity of members of the
Holophaga–Acidobacterium group, which is composed of sequences of yet-uncultivated microorganisms, is confirmed. The plant roots have a selective effect towards the gamma
Proteobacteria, to the detriment of the Gram-positive and the
Holophaga–Acidobacterium bacteria, leading to a dominance of
Pseudomonas. This work shows by a culture independent approach that the phylogenetic diversity decreases in the proximity of plant roots.
Spores of the arbuscular mycorrhizal fungi (AMF) Glomus geosporum and Glomus constrictum were harvested from single-spore-derived pot cultures with either Plantago lanceolata or Hieracium pilosella ...as host plants. PCR-denaturing gradient gel electrophoresis analysis revealed that the bacterial communities associated with the spores depended more on AMF than host plant identity. The composition of the bacterial populations linked to the spores could be predominantly influenced by a specific spore wall composition or AMF exudate rather than by specific root exudates. The majority of the bacterial sequences that were common to both G. geosporum and G. constrictum spores were affiliated with taxonomic groups known to degrade biopolymers (Cellvibrio, Chondromyces, Flexibacter, Lysobacter, and Pseudomonas). Scanning electron microscopy of G. geosporum spores revealed that these bacteria are possibly feeding on the outer hyaline spore layer. The process of maturation and eventual germination of AMF spores might then benefit from the activity of the surface microorganisms degrading the outer hyaline wall layer.
In tropical ecosystems, termite mound soils constitute an important soil compartment covering around 10% of African soils. Previous studies have shown (S. Fall, S. Nazaret, J. L. Chotte, and A. ...Brauman, Microb. Ecol. 28:191-199, 2004) that the bacterial genetic structure of the mounds of soil-feeding termites (Cubitermes niokoloensis) is different from that of their surrounding soil. The aim of this study was to characterize the specificity of bacterial communities within mounds with respect to the digestive and soil origins of the mound. We have compared the bacterial community structures of a termite mound, termite gut sections, and surrounding soil using PCR-denaturing gradient gel electrophoresis (DGGE) analysis and cloning and sequencing of PCR-amplified 16S rRNA gene fragments. DGGE analysis revealed a drastic difference between the genetic structures of the bacterial communities of the termite gut and the mound. Analysis of 266 clones, including 54 from excised bands, revealed a high level of diversity in each biota investigated. The soil-feeding termite mound was dominated by the Actinobacteria phylum, whereas the Firmicutes and Proteobacteria phyla dominate the gut sections of termites and the surrounding soil, respectively. Phylogenetic analyses revealed a distinct clustering of Actinobacteria phylotypes between the mound and the surrounding soil. The Actinobacteria clones of the termite mound were diverse, distributed among 10 distinct families, and like those in the termite gut environment lightly dominated by the Nocardioidaceae family. Our findings confirmed that the soil-feeding termite mound (C. niokoloensis) represents a specific bacterial habitat in the tropics.
White lupin (Lupinus albus L. cv. Amiga) reacts to phosphate deficiency by producing cluster roots which exude large amounts of organic acids. The detailed knowledge of the excretion physiology of ...the different root parts makes it a good model plant to study plant-bacteria interaction. Since the effect of the organic acid exudation by cluster roots on the rhizosphere microflora is still poorly understood, we investigated the abundance, diversity and functions of bacteria associated with the cluster roots of white lupin, with special emphasis on the influence of root proximity (comparing root, rhizosphere soil and bulk soil fractions) and cluster root growth stages, which are characterized by different excretion activities. Plants were grown for five weeks in microcosms, in the presence of low phosphate concentrations, on acidic sand inoculated with a soil suspension from a lupin field. Plate counts showed that bacterial abundance decreased at the stage where the cluster root excretes high amounts of citrate and protons. In vitro tests on isolates showed that the frequencies of auxin producers were highest in juvenile and mature cluster roots and significantly decreased in senescent cluster roots. However, no significant difference in the frequency of auxin producers was found between cluster and non cluster roots. The diversity and structure of bacterial communities were investigated by DGGE of 16S rDNA and 16S rRNA. The diversity and community structure were mostly influenced by root proximity and, to a lesser extent, by cluster root stage. The richness of bacterial communities decreased with root proximity, whereas the proportion of active populations increased. The high citrate and proton excretion occurring at the mature stage of cluster roots had a strong impact on the structure and richness of the bacterial communities, both in the root and in the rhizosphere soil.
Summary
The oxalate–carbonate pathway involves the oxidation of calcium oxalate to low‐magnesium calcite and represents a potential long‐term terrestrial sink for atmospheric CO
2. In this pathway, ...bacterial oxalate degradation is associated with a strong local alkalinization and subsequent carbonate precipitation. In order to test whether this process occurs in soil, the role of bacteria, fungi and calcium oxalate amendments was studied using microcosms. In a model system with sterile soil amended with laboratory cultures of oxalotrophic bacteria and fungi, the addition of calcium oxalate induced a distinct pH shift and led to the final precipitation of calcite. However, the simultaneous presence of bacteria and fungi was essential to drive this pH shift. Growth of both oxalotrophic bacteria and fungi was confirmed by qPCR on the frc (oxalotrophic bacteria) and 16S rRNA genes, and the quantification of ergosterol (active fungal biomass) respectively. The experiment was replicated in microcosms with non‐sterilized soil. In this case, the bacterial and fungal contribution to oxalate degradation was evaluated by treatments with specific biocides (cycloheximide and bronopol). Results showed that the autochthonous microflora oxidized calcium oxalate and induced a significant soil alkalinization. Moreover, data confirmed the results from the model soil showing that bacteria are essentially responsible for the pH shift, but require the presence of fungi for their oxalotrophic activity. The combined results highlight that the interaction between bacteria and fungi is essential to drive metabolic processes in complex environments such as soil.
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