Complete genome sequence of "Enterobacter lignolyticus" SCF1

In an effort to discover anaerobic bacteria capable of lignin degradation, we isolated "Enterobacter lignolyticus" SCF1 on minimal media with alkali lignin as the sole source of carbon. This organism was isolated anaerobically from tropical forest soils collected from the Short Cloud Forest site in the El Yunque National Forest in Puerto Rico, USA, part of the Luquillo Long-Term Ecological Research Station. At this site, the soils experience strong fluctuations in redox potential and are net methane producers. Because of its ability to grow on lignin anaerobically, we sequenced the genome. The genome of "E. lignolyticus" SCF1 is 4.81 Mbp with no detected plasmids, and includes a relatively small arsenal of lignocellulolytic carbohydrate active enzymes. Lignin degradation was observed in culture, and the genome revealed two putative laccases, a putative peroxidase, and a complete 4-hydroxyphenylacetate degradation pathway encoded in a single gene cluster.     

Draft genome sequence of the sulfur-oxidizing bacterium "Candidatus Sulfurovum sediminum" AR, which belongs to the Epsilonproteobacteria

Sulfur-oxidizing bacteria are common microorganisms in a variety of sulfide-rich environments. They play important roles in the global sulfur cycle on earth. Here, we present a high-quality draft genome sequence of a sulfur-oxidizing bacterium, "Candidatus Sulfurovum sediminum" strain AR, which belongs to the class Epsilonproteobacteria and dominated an enrichment culture from a marine sediment collected off Svalbard, within the Arctic Circle. Its genome contains genes for sulfur oxidation and carbon fixation. The size of the draft genome is 2.12 Mb, and the G+C content is 39.4%.     

Genome sequence of "Candidatus Nitrosopumilus salaria" BD31, an ammonia-oxidizing archaeon from the San Francisco Bay estuary

Ammonia-oxidizing archaea (AOA) play important roles in nitrogen and carbon cycling in marine and terrestrial ecosystems. Here, we present the draft genome sequence for the ammonia-oxidizing archaeon "Candidatus Nitrosopumilus salaria" BD31, which was enriched in culture from sediments of the San Francisco Bay estuary. The genome sequences revealed many similarities to the genome of Nitrosopumilus maritimus.     

Optimization of biofloc production in <Emphasis Type="Italic">Azospirillum brasilense</Emphasis> (MTCC-125) and evaluation of its adherence with the roots of certain crops

The phenomenon of flocculation in Azospirillum brasilense (MTCC-125) was studied under different combinations of carbon and nitrogen sources. Fructose and Potassium nitrate at a pH of 6.4 in the cultural medium favour a higher bio-floc production. The biofloc was studied for root adhesion and its survival efficiency in the rhizoplane and rhizosphere of certain crops such as sorghum and sunflower under dryland condition. It has been demonstrated that the flocculated cultures of Azospirillum were found to have maximum adhesion to the root surface and higher survival rate in the rhizoplane and rhizosphere under different moisture stressed conditions as compared to the log phase cells of Azospirillum.     

Comparative genomics of "Dehalococcoides ethenogenes" 195 and an enrichment culture containing unsequenced "Dehalococcoides" strains

Tetrachloroethene (PCE) and trichloroethene (TCE) are prevalent groundwater contaminants that can be completely reductively dehalogenated by some "Dehalococcoides" organisms. A Dehalococcoides-organism-containing microbial consortium (referred to as ANAS) with the ability to degrade TCE to ethene, an innocuous end product, was previously enriched from contaminated soil. A whole-genome photolithographic microarray was developed based on the genome of "Dehalococcoides ethenogenes" 195. This microarray contains probes designed to hybridize to >99% of the predicted protein-coding sequences in the strain 195 genome. DNA from ANAS was hybridized to the microarray to characterize the genomic content of the ANAS enrichment. The microarray results revealed that the genes associated with central metabolism, including an apparently incomplete carbon fixation pathway, cobalamin-salvaging system, nitrogen fixation pathway, and five hydrogenase complexes, are present in both strain 195 and ANAS. Although the gene encoding the TCE reductase, tceA, was detected, 13 of the 19 reductive dehalogenase genes present in strain 195 were not detected in ANAS. Additionally, 88% of the genes in predicted integrated genetic elements in strain 195 were not detected in ANAS, consistent with these elements being genetically mobile. Sections of the tryptophan operon and an operon encoding an ABC transporter in strain 195 were also not detected in ANAS. These insights into the diversity of Dehalococcoides genomes will improve our understanding of the physiology and evolution of these bacteria, which is essential in developing effective strategies for the bioremediation of PCE and TCE in the environment.     

Measurement of rhizosphere respiration and organic matter decomposition using natural 13C

Due to the limitations in methodology it has been a difficult task to measure rhizosphere respiration and original soil carbon decomposition under the influence of living roots. ¹⁴C-labeling has been widely used for this purpose in spite of numerous problems associated with the labeling method. In this paper, a natural ¹³C method was used to measure rhizosphere respiration and original soil carbon decomposition in a short-term growth chamber experiment. The main objective of the experiment was to validate a key assumption of this method: the ¹³C value of the roots represents the ¹³C value of the rhizosphere respired CO₂. Results from plants grown in inoculated carbon-free medium indicated that this assumption was valid. This natural ¹³C method was demonstrated to be advantageous for studying rhizosphere respiration and the effects of living roots on original soil carbon decomposition.     

Genome and methylome of the oleaginous diatom <Emphasis Type="Italic">Cyclotella cryptica</Emphasis> reveal genetic flexibility toward a high lipid phenotype

Background

Improvement in the performance of eukaryotic microalgae for biofuel and bioproduct production is largely dependent on characterization of metabolic mechanisms within the cell. The marine diatom Cyclotella cryptica, which was originally identified in the Aquatic Species Program, is a promising strain of microalgae for large-scale production of biofuel and bioproducts, such as omega-3 fatty acids.

Results

We sequenced the nuclear genome and methylome of this oleaginous diatom to identify the genetic traits that enable substantial accumulation of triacylglycerol. The genome is comprised of highly methylated repetitive sequence, which does not significantly change under silicon starved lipid induction, and data further suggests the primary role of DNA methylation is to suppress DNA transposition. Annotation of pivotal glycolytic, lipid metabolism, and carbohydrate degradation processes reveal an expanded enzyme repertoire in C. cryptica that would allow for an increased metabolic capacity toward triacylglycerol production. Identification of previously unidentified genes, including those involved in carbon transport and chitin metabolism, provide potential targets for genetic manipulation of carbon flux to further increase its lipid phenotype. New genetic tools were developed, bringing this organism on a par with other microalgae in terms of genetic manipulation and characterization approaches.

Conclusions

Functional annotation and detailed cross-species comparison of key carbon rich processes in C. cryptica highlights the importance of enzymatic subcellular compartmentation for regulation of carbon flux, which is often overlooked in photosynthetic microeukaryotes. The availability of the genome sequence, as well as advanced genetic manipulation tools enable further development of this organism for deployment in large-scale production systems.

     

"Candidatus Cloacamonas acidaminovorans": genome sequence reconstruction provides a first glimpse of a new bacterial division

Many microorganisms live in anaerobic environments. Most of these microorganisms have not yet been cultivated. Here, we present, from a metagenomic analysis of an anaerobic digester of a municipal wastewater treatment plant, a reconstruction of the complete genome of a bacterium belonging to the WWE1 candidate division. In silico proteome analysis indicated that this bacterium might derive most of its carbon and energy from the fermentation of amino acids, and hence, it was provisionally classified as "Candidatus Cloacamonas acidaminovorans." "Candidatus Cloacamonas acidaminovorans" is probably a syntrophic bacterium that is present in many anaerobic digesters. This report highlights how environmental sequence data might provide genomic and functional information about a new bacterial clade whose members are involved in anaerobic digestion.     

Nitrogen fixation in seagrass meadows: Regulation, plant–bacteria interactions and significance to primary productivity

The rhizosphere sediments of seagrasses are generally a site of intense nitrogen fixation activity and this can provide a significant source of "new" nitrogen for the growth of the plants. In this paper, I review the data concerning nitrogen fixation in seagrass ecosystems, the transfer of the fixed nitrogen from the bacteria to the plants and its contribution to the overall productivity of seagrasses in different climatic zones.
The relationship between the plants and diazotrophic heterotrophic bacteria in the rhizosphere is discussed, particularly focusing on the potentially important role of nitrogen-fixing, sulphate-reducing bacteria. The regulation of nitrogen fixation rates in the rhizosphere by photosynthetically driven oxygen and fixed carbon release by the plant roots and rhizomes, and the availability of ammonium in the porewater, is assessed. Finally, the hypothesis that a mutualistic or symbiotic association exists between the seagrasses and heterotrophic nitrogen fixers in the rhizosphere, based on the mutual exchange of fixed carbon and nitrogen, is discussed.     

Rhizosphere carbon flow measurement and implications: from isotopes to reporter genes

Despite the fundamental importance of rhizosphere C-flow in managed and natural systems, reliable measurement/resolution of C-flow and assessment of its consequences have largely remained elusive to soil biologists. Techniques involving both radioactive (¹⁴C) and stable (¹³C) isotopes of carbon have made some progress in terms of studying rhizosphere C-flow. Pulse-chase techniques have been used effectively to study dynamics of C-transfer to the rhizosphere and rhizosphere microbial biomass. The information obtained through pulse-chase is strongly dependent on the chase period following the labelling event. Continuous labelling is primarily used to determine plant inputs to soil over an extended time period and includes all kinds of C input – from root turnover, root respiration, root exudation, production of mucilage, etc. One of the main constraints to both approaches is that distinguishing root from microbial respiration is difficult, if not impossible. ¹³C techniques have gone some way towards resolving this difficulty, although ¹³C signatures in the plant–soil system are not easy to interpret and detailed resolution of carbon flow through different components of the rhizosphere biomass is unlikely to be achieved in such an inherently `noisy' system. Recent developments in molecular biology now provide a new opportunity to resolve rhizosphere C-flow and its implications. Reporter gene systems where, for example, rhizobacteria are marked with lux and unstable gfp reporters, overcome the difficulty of distinguishing root and microbial C fluxes and complement the isotopic and more traditional approaches. Reporter systems have now begun to resolve the competitive C sink strengths of different components of the rhizosphere microbial community and assess how a rhizobacterial inoculum may change C-flow in applications such as disease control and rhizoremediation of contaminated land. Fusion of reporter genes to nutrient (N and P) starvation genes in rhizobacteria has also enabled in situ characterisation of nutrient depletion around the root and assessment of the impact of changes in C-flow (such as those induced by climate change) on nutrient depletion dynamics. The availability of an integrated approach involving isotopic, molecular biological and other techniques now offers an exciting new era where reliable measurement and resolution of rhizosphere C-flow (and its consequences) can contribute to our understanding of ecosystem function and to management of crop-microbe interactions.     

Tripartite interactions among <Emphasis Type="Italic">Paenibacillus lentimorbus</Emphasis> NRRL B-30488, <Emphasis Type="Italic">Piriformospora indica</Emphasis> DSM 11827, and <Emphasis Type="Italic">Cicer arietinum</Emphasis> L.

Tripartite interactions among Paenibacillus lentimorbus NRRL B-30488 (B-30488), Piriformospora indica DSM 11827 (DSM 11827) and their consortia (B-30488:DSM 11827:: 1:1) with native rhizobial population in the rhizosphere of Cicer arietinum L. (Chick pea) was tested for enhancing nodulations and plant growth promotion. Number of nodules and dry weight per plant significantly enhanced (P = 0.05), which is further evident by N, P, and K uptake by plants and were found to be maximum in B-30488 treated followed by B-30488: DSM 11827 and DSM 11827, as compared with uninoculated control, in 60 days grown chickpea plants. Microbial community structure in the rhizosphere of the four treatments was assessed, using Biolog Eco and MT plates. Principal component analysis (PCA) of carbon source utilization pattern on Biolog Eco plates did not show any clustering among the four samples indicating that in case of individually DSM 11827 and B-30488 treated chickpea rhizosphere there was significant change in microbial community structure, compared with lesser changes in un-inoculated and B-30488 and DSM 11827 consortium treated chickpea rhizosphere microflora. Additional carbon sources tested using Biolog MT plates, higher activity of lignin, chitin, and cellulose utilizing microbial communities in the rhizosphere being stimulated by root exudates treated with B-30488 alone or in consortia with DSM 11827, and, in turn, should encourage beneficial symbiotic or mutualistic microorganisms that can act as plant growth promoting and biocontrol agents.     

A critical review of labelling techniques used to quantify rhizosphere carbon-flow

The rhizosphere is a major sink for photo-assimilated carbon and quantifying inputs into this sink is one of the main goals of rhizosphere biology as organic carbon lost from plant roots supports a higher microbial population in the rhizosphere compared to bulk soil. Two fundamentally different¹⁴CO₂ labelling strategies have been developed to estimate carbon fluxes through the rhizosphere — continuous feeding of shoots with labelled carbon dioxide and pulse-chase experiments. The biological interpretation that can be placed on the results of labelling experiments is greatly biased by the technique used. It is the purpose of this paper to assess the advantages, disadvantages and the biological interpretation of both continuous and pulse labelling and to consider how to partition carbon fluxes within the rhizosphere.     

Engineering Root Exudation of <Emphasis Type="Italic">Lotus</Emphasis> toward the Production of Two Novel Carbon Compounds Leads to the Selection of Distinct Microbial Populations in the Rhizosphere

The culture of opine-producing transgenic Lotus plants induces the increase in the rhizosphere of bacterial communities that are able to utilize these molecules as sole carbon source. We used transgenic Lotus plants producing two opines, namely mannopine and nopaline, to characterize the microbial communities directly influenced by the modification of root exudation. We showed that opine-utilizers represent a large community in the rhizosphere of opine-producing transgenic Lotus. This community is composed of at least 12 different bacterial species, one third of which are able to utilize the opine mannopine and two thirds the opine nopaline. Opine utilizers are diverse, belonging to the Gram-positive and -negative bacteria. We described two novel mannopine-utilizing species, Rhizobium and Duganella spp., and five novel nopaline-utilizing species, Duganella, Afipia, Phyllobacterium, Arthrobacter, and Bosea spp. Although opine utilizers mostly belong to the -Proteobacteria, Rhizobiaceae family, there is little overlap between the populations able to utilize each of the two opines produced by the plants. Noticeably, in the rhizosphere of transgenic Lotus, only the opine mannopine favors the growth of Agrobacterium tumefaciens, the bacterium from which opines have been characterized. The diversity of opine utilizers from the rhizosphere of Lotus plants is greater than that observed from any other environment. Therefore, transgenic plants with engineered exudation constitute an excellent tool to isolate and characterize specific microbial populations.     

异裂菊属根际微生物群落结构及功能多样性

异裂菊属是广西喀斯特石山区典型的特有属,根际微生物是其能否有效吸收、有效利用土壤养分和适应石山恶劣土壤环境的最直接表征之一。该研究采用DGGE和Biolog两种方法对异裂菊属植物根际和非根际微生物多样性进行了研究。结果表明:(1)异裂菊属5个种根际pH、碱解氮等9个养分含量都高于非根际。(2)5个种的根际、非根际存在2个共有细菌类群,但在数量上存在差异,3个种的根际条带小于非根际;5个种的根际、非根际微生物群落较为相似,较易聚在一起。(3)绢叶异裂菊根际微生物对碳源利用能力最强,凹脉异裂菊非根际最弱,其他对碳源的利用能力较接近;异裂菊属种根际微生物利用碳源的能力都高于非根际,根际微生物多样性指数均高于非根际,优势度指数与非根际基本相同或略高于非根际,丰富度和均匀度指数与优势度指数规律相似;异裂菊属根际、非根际微生物利用的碳源主要是糖类、羧酸类和氨基酸类化合物,4个种根际微生物利用碳源的能力高于非根际。(4)阳离子交换量、黏粒含量百分率和碱解氮是影响异裂菊属根际微生物碳源利用模式的最重要因子。总体来说,土壤理化性质对异裂菊属植物根际微生物群落多样性具有重要影响,异裂菊属通过分泌羧酸、糖等多类化合物提高了根际微生物的活性,进而有效地提高了根际肥力水平。     

夜间增温和施肥对川西亚高山针叶林两种树苗根际效应的影响

开展植物根际效应对全球变化响应的研究是深入认识根际微生态系统中植物根系与土壤微生物相互作用过程及机制的关键。以川西亚高山针叶林两种主要树种幼苗--云杉(Picea asperata)和岷江冷杉(Abies faxoniana)为研究材料,采用红外辐射模拟增温和外施NH₄NO₃氮肥的方法,研究了夜间增温和施肥对两种幼苗根际效应的影响。结果表明:红外辐射增温导致气温增加了1.62 ℃,土壤5 cm和10 cm层月均温度显著增加了2.89 ℃和3.10℃。增温和施肥处理对两种幼苗不同参数根际效应的影响各不相同,表现为不同程度的正根际效应、负根际效应或者无影响。增温使云杉幼苗根际与非根际土SMB-C含量均显著增加(分别为42.28%和31.02%),非根际土有机碳含量降低了7.03%;而增温对两种幼苗土壤肥力因素根际效应的影响总体并不显著,增温仅对云杉全氮有显著的负根际效应(79.43%),而岷江冷杉通过根际土全氮和SMB-N含量的增加,其根际效应大小在增温处理下显著增强。施肥处理和两因子的联合作用显著提高了两种幼苗的NO^-₃-N、NH⁺₄-N和云杉非根际土SMB-N含量,并使岷江冷杉NH⁺₄-N表现出正根际效应,而云杉SMB-N表现出明显的负根际效应(120.80%和253.06%)。这种响应差异可能与不同植物种类地下碳分配及其植物根系所吸收的养分有关,从而赋予了不同植物种类在未来全球变化背景下可能具有不同的适应力和竞争优势,并进一步对亚高山针叶林地下过程及其早期更新产生潜在影响。     

Assessment of functional diversity and structure of phytate-hydrolysing bacterial community in <Emphasis Type="Italic">Lolium perenne</Emphasis> rhizosphere

Background and aims

Plant growth is frequently limited by the availability of inorganic phosphorus (P) in the soil. In most soils, a considerable amount of the soil P is bound to organic molecules. Of these, phytate is the most abundant identifiable organic P form, but is not readily available to plants. In contrast, microorganisms have been shown to degrade phytate with high efficiency. The current study aims to characterize the members of the phytate-hydrolysing bacterial community in rhizosphere, and the molecular and enzymatic ability of these bacteria to degrade phytate.

Methods and results

The phytate-hydrolysing bacterial community was characterized from the rhizosphere of plants cultivated in the presence or absence of phytate supplementation. Major changes in the bacterial community structure were observed with both culture-dependent and -independent methods, which highlighted the predominance of Proteobacteria and Actinobacteria. Phytase activity was detected for a range of rhizobacterial isolates as well as the presence of, β-propeller phytases (BPP) for both isolates and directly in a soil sample.

Conclusion

A wide taxonomic range of functional phytate utilizers have been discovered, in soil bacterial taxa that were previously not well known for their ability to utilise phytate as P or C sources. This study provides new insights into microbial carbon and phosphorus cycling in soil.

     

Response of rhizosphere microbial communities associated with Antarctic hairgrass (<Emphasis Type="Italic"> Deschampsia antarctica</Emphasis><Emphasis Type="Underline">)</Emphasis> to UV radiation

The response of rhizosphere microbial communities associated with natural populations of Deschampsia antarctica growing on Léonie Island (67°36S, 68°21W, Antarctic Peninsula) to UV radiation was investigated. UV radiation was controlled in the field using Perspex VA screens (UV-B opaque) which transmit little radiation below 380 nm but allow penetration of approximately 92% of radiation above 400 nm, and Perspex OXO2 screens (UV-B transparent) which transmit approximately 70% of radiation at 280 nm, rising to 90% at 300 nm and above. Reducing ambient UV radiation altered the phenotypic profile of the rhizosphere microbial community. This alteration was expressed as enhanced carbohydrate and carboxylic acid utilisation by the rhizosphere micro-organisms. It is hypothesised that ambient levels of UV radiation indirectly affect rhizosphere micro-organisms by influencing the quality or quantity of root exudates.     

Partitioning of belowground C in young sugar maple forest

Background and aims

Trees allocate a high proportion of assimilated carbon belowground, but the partitioning of that C among ecosystem components is poorly understood thereby limiting our ability to predict responses of forest C dynamics to global change drivers.

Methods

We labeled sugar maple saplings in natural forest with a pulse of photosynthetic ¹³C in late summer and traced the pulse over the following 3 years. We quantified the fate of belowground carbon by measuring ¹³C enrichment of roots, rhizosphere soil, soil respiration, soil aggregates and microbial biomass.

Results

The pulse of ¹³C contributed strongly to root and rhizosphere respiration for over a year, and respiration comprised about 75 % of total belowground C allocation (TBCA) in the first year. We estimate that rhizosphere carbon flux (RCF) during the dormant season comprises at least 6 % of TBCA. After 3 years, 3.8 % of the C allocated belowground was recovered in soil organic matter, mostly in water-stable aggregates.

Conclusions

A pulse of carbon allocated belowground in temperate forest supplies root respiration, root growth and RCF throughout the following year and a small proportion becomes stabilized in soil aggregates.