Plant-mediated methane emission from an Indian mangrove

Mangroves have been considered for a long time to be a minor methane source, but recent reports have shown that polluted mangroves may emit substantial amounts of methane. In an unpolluted Indian mangrove, we measured annual methane emission rates of 10 g CH₄ yr^?1 from the stands of Avicennia marina. This rate is of the same order of magnitude as rates from Northern wetlands. Methane emission from a freshwater‐influenced area was higher, but was lower from a stunted mangrove growing on a hypersaline soil. Methane emission was mediated by the pneumatophores of Avicennia. This was consistent with the methane concentration in the aerenchyma, which decreased on average from 350 ppm_v in the cable roots to 10 ppm_v in the emergent part of the pneumatophores. However, the number of pneumatophores varied seasonally. The minimum number occurred during the monsoon season, which reduced methane emissions largely. Ebullition from unvegetated areas may also be important, at least during monsoon season when measured bubble fluxes were occasionally about five times as high as pneumatophore‐mediated emissions.     

Soil microbes and the availability of soil nutrients

It is likely to provide plants with their necessary nutrients using chemical and biological fertilization. Although chemical fertilization is a quick method, it is not recommendable economically and environmentally, especially if overused. Biological fertilization is the use of soil microbes including arbuscular mycorrhizal fungi and plant growth promoting rhizobacteria to inoculate plants. It has been proved that biological fertilization is an efficient method to supply plants with their necessary nutrients. It is economically and environmentally recommendable, because it results in sustainability. In this article, some of the most important details including the mechanisms and processes regarding the effects of soil microbes on the availability and hence uptake of nutrients by plant are reviewed. Such details can be important for the selection and hence production of microbial inoculums, which are appropriate for biological fertilization.     

Effects of labile soil carbon on nutrient partitioning between an arctic graminoid and microbes

We measured partitioning of N and P uptake between soil microorganisms and potted Festuca vivipara in soil from a subarctic heath in response to factorial addition of three levels of labile carbon (glucose) combined with two levels of inorganic N and P. The glucose was added to either non-sterilized or sterilized (autoclaved) soils in quantities which were within the range of reported, naturally occurring amounts of C released periodically from the plant canopy. The aims were, firstly, to examine whether the glucose stimulated microbial nutrient uptake to the extent of reducing plant nutrient uptake. This is expected in nutrient-deficient soils if microbes and plants compete for the same nutrients. Secondly, we wanted to test our earlier␣interpretation that growth reduction observed in graminoids after addition of leaf extracts could be caused directly by labile carbon addition, rather than by phytotoxins in the extracts. Addition of high amounts of N did not affect the microbial N pool, whereas high amounts of added P significantly increased the microbial P pool, indicating a luxury P uptake in the microbes. Both plant N and in particular P uptake increased strongly in response to soil sterilization and to addition of extra N or P. The increased␣uptake led to enhanced plant growth when both elements were applied in high amounts, but only led to increased tissue concentrations without growth responses when the nutrients were added separately. Glucose had strong and contrasting effects on plant and microbial N and P uptake. Microbial N and P uptake increased, soil inorganic N and P concentrations were reduced and plant N and P uptake declined when glucose was added. The responses were dose-dependent within the range of 0–450 μg C g⁻¹ soil added to the non-sterilized soil. The opposite responses of plants and microbes showed that plant acquisition of limiting nutrients is dependent on release of nutrients from the soil microbes, which is under strong regulation by the availability and microbial uptake of labile C. Hence, we conclude, firstly, that the microbial populations can compete efficiently with plants for nutrients to an extent of affecting plant growth when the microbial access to labile carbon is high in nutrient deficient soils. We also conclude that reduced growth of plants after addition of leaf extracts to soil can be caused by carbon-induced shifts in nutrient partitioning between plants and microbes, and not necessarily by phytotoxins added with the extracts as suggested by some experiments. Received: 15 February 1997 / Accepted: 12 July 1997     

Enrichment and characterization of an anaerobic cellulolytic microbial consortium SQD-1.1 from mangrove soil

Enrichment of microbial consortia provides an approach to simulate and investigate microbial communities in natural environments. In this study, a cellulolytic microbial consortium SQD-1.1 was enriched from mangrove soil of Qinglan port (Hainan, China) by 27 times continuous subcultivation under anaerobic static conditions. The consortium could completely degrade 0.2 % (w/v) filter paper within 3 days and utilized it as the sole carbon source. PCR-denaturing gradient gel electrophoresis analysis revealed a stable microbial community structure in the incubation process of 10 days and in the procedure of subcultivation. Twenty-four operational taxonomic units belonging to seven phyla were obtained from the full-length 16S rRNA gene library. Five clones, closest related to the genera Alkaliflexus, Clostridium, Alistipes, Spirochaeta, and Trichococcus, were the predominant ones. Among them, M117, phylogeneticly showing high similarity (16S rRNA gene identity, 95.3 %) with the cellulolytic anaerobic bacterium Clostridium straminisolvens CSK1^T, was the potential key cellulolytic bacterium. Using the plate cultivation method, 12 strains, including one potential new species and four potential new species of new genera, were isolated. The strain P2, corresponding to the most frequently detected clone (M05) in the 16S rRNA gene library, showed both CMCase and xylanase activity and may be another important cellulolytic bacterium. The findings of cellulase activity in cell pellet and cohesion and dockerin domains in metagenome data further suggested the potential of utilization of cellulosomes by the consortium to degrade cellulose. Consortium SQD-1.1 provides a candidate for investigating the mechanism of cellulose degradation under anoxic conditions in natural environments.     

Effects of mercury compounds on soil microbes

Summary Even low concentrations of mercury compounds in agar media strongly decreased the number of soil microbes that could be isolated on these media.Mercury compounds added to the soil in very high concentrations inhibited CO₂-evolution, dehydrogenase activity, and nitrification. In contrast, the number of microbes increased somewhat in a clay soil treated with HgCl₂. Phenylmercury acetate had a stronger inhibiting effect than HgCl₂. In sandy soil the microbial processes were inhibited more strongly than in clay soil.Mercury compounds present in the soil or added in low concentrations are not expected to seriously disturb organic-matter breakdown, nitrogen mineralization, or the soil-microbe numbers.     

土壤微生物RAPD分析体系的优化研究

采用正交实验设计,对影响土壤微生物RAPD扩增体系的Mg2+、dNTP浓度及引物浓度进行了研究,同时对退火温度、延伸时间及循环次数进行摸索。结果表明,适宜土壤微生物PCR扩增反应在25μl体积中进行,包括7ng土壤微生物DNA样品、20pm随机引物l、.5uTaq酶、3.0mmol.L-1Mg-CL2和0.2mmol.L-1dNTP。PCR扩增反应进程如下:94℃3min,使土壤DNA变性;然后再进行39个循环,每个循环包括94℃1min,37℃40s,72℃90s,结束后72℃延伸7min。     

Soil salinity and pH in Japanese mangrove forests and growth of cultivated mangrove plants in different soil conditions

Soil conditions of mangrove forests in southern Japan were found to correlate largely with zonal distributions of the species.Kandelia candel grew in soils with low salinity and low pH,Avicennia marina, Rhizophora stylosa andSonneratia alba in soils with high salinity and high pH, andBruguiera gymnorrhiza in soil with a wide range of pH but limited range of salinity.Lumnitzera racemosa colonized soil with a wide range of pH and medium salinity. Seedlings ofKandelia candel, Bruguiera gymnorrhiza andRhizophora stylosa were planted in soils with differing salinity and pH. Optimum seedling growth ofKandelia, Bruguiera andRhizophora occurred when plants were cultivated in soils similar to those of their natural habitats, suggesting that growth of mangrove species and their zonal distributions were regulated by salinity and soil pH.     

The role of soil microbes in plant sulphur nutrition

Chemical and spectroscopic studies have shown that in agricultural soils most of the soil sulphur (>95%) is present as sulphate esters or as carbon-bonded sulphur (sulphonates or amino acid sulphur), rather than inorganic sulphate. Plant sulphur nutrition depends primarily on the uptake of inorganic sulphate. However, recent research has demonstrated that the sulphate ester and sulphonate-pools of soil sulphur are also plant-bioavailable, probably due to interconversion of carbon-bonded sulphur and sulphate ester-sulphur to inorganic sulphate by soil microbes. In addition to this mineralization of bound forms of sulphur, soil microbes are also responsible for the rapid immobilization of sulphate, first to sulphate esters and subsequently to carbon-bound sulphur. The rate of sulphur cycling depends on the microbial community present, and on its metabolic activity, though it is not yet known if specific microbial species or genera control this process. The genes involved in the mobilization of sulphonate- and sulphate ester-sulphur by one common rhizosphere bacterium, Pseudomonas putida, have been investigated. Mutants of this species that are unable to transform sulphate esters show reduced survival in the soil, indicating that sulphate esters are important for bacterial S-nutrition in this environment. P. putida S-313 mutants that cannot metabolize sulphonate-sulphur do not promote the growth of tomato plants as the wild-type strain does, suggesting that the ability to mobilize bound sulphur for plant nutrition is an important role of this species.     

Characterization of trapped lignin-degrading microbes in tropical forest soil

Lignin is often the most difficult portion of plant biomass to degrade, with fungi generally thought to dominate during late stage decomposition. Lignin in feedstock plant material represents a barrier to more efficient plant biomass conversion and can also hinder enzymatic access to cellulose, which is critical for biofuels production. Tropical rain forest soils in Puerto Rico are characterized by frequent anoxic conditions and fluctuating redox, suggesting the presence of lignin-degrading organisms and mechanisms that are different from known fungal decomposers and oxygen-dependent enzyme activities. We explored microbial lignin-degraders by burying bio-traps containing lignin-amended and unamended biosep beads in the soil for 1, 4, 13 and 30 weeks. At each time point, phenol oxidase and peroxidase enzyme activity was found to be elevated in the lignin-amended versus the unamended beads, while cellulolytic enzyme activities were significantly depressed in lignin-amended beads. Quantitative PCR of bacterial communities showed more bacterial colonization in the lignin-amended compared to the unamended beads after one and four weeks, suggesting that the lignin supported increased bacterial abundance. The microbial community was analyzed by small subunit 16S ribosomal RNA genes using microarray (PhyloChip) and by high-throughput amplicon pyrosequencing based on universal primers targeting bacterial, archaeal, and eukaryotic communities. Community trends were significantly affected by time and the presence of lignin on the beads. Lignin-amended beads have higher relative abundances of representatives from the phyla Actinobacteria, Firmicutes, Acidobacteria and Proteobacteria compared to unamended beads. This study suggests that in low and fluctuating redox soils, bacteria could play a role in anaerobic lignin decomposition.     

Interaction of soil microbes with mycorrhizal fungi in tomato

In this study, the interaction of soil microbes with mycorrhizal fungi (MF) was performed to understand the effect on tomato. A pot and a field experiment were employed to investigate the impact of soil microbes i.e. Fusarium oxysporum f. sp. lycopersici, Trichoderma harzianum, Aspergillus niger and Rhizobium leguminosarum, on AM fungi in pots and field studies. The soils without microbes which treated controls with or without mycorrhizal inoculation were also included. Plant growth and root colonisation were measured 36, 75 and 120?days post inoculation (dpi) in the both pot experiment and field study. Soil microbes’ effects on the growth behaviour of the tomato plant were determined via the shoot and root weight. R. leguminosarum and A. niger did not affect the colonisation ability much, but F. oxysporum f. sp. lycopersici and T. harzianum resulted in the inhibition of AM fungal colonisation in both pot and field studies. Our study provides evidence for the effects of soil microbes on the diversity of AM fungi and their effect on the tomato plants. The higher concentrations of phosphorus and of proteins in the root tissues, previously colonised with AM fungi, point out their effect as biofertilizers, according to the concept of sustainable agriculture.     

Changes in soil iron biogeochemistry in response to mangrove dieback

Biogeochemistry - Fe biogeochemistry is associated with important ecosystem services provided by mangrove forests, including carbon sequestration and the retention of potentially toxic elements....     

Biogeochemical effects of simulated sea level rise on carbon loss in an Everglades mangrove peat soil

Saltwater intrusion and inundation can affect soil microbial activity, which regulates the carbon (C) balance in mangroves and helps to determine if these coastal forests can keep pace with sea level rise (SLR). This study evaluated the effects of increased salinity (+15 ppt), increased inundation (?8 cm), and their combination, on soil organic C loss from a mangrove peat soil (Everglades, Florida, USA) under simulated tides. Soil respiration (CO₂ flux), methane (CH₄) flux, dissolved organic carbon (DOC) production, and porewater nutrient concentrations were quantified. Soil respiration was the major pathway of soil organic C loss (94–98%) and was approximately 90% higher in the control water level than the inundated treatment under elevated salinity. Respiration rate increased with water temperature, but depended upon salinity and tidal range. CH₄ flux was minimal, while porewater DOC increased with a concomitant, significant decline in soil bulk density under increased inundation. Porewater ammonium increased (73%) with inundation and soluble reactive phosphorus increased (32%) with salinity. Overall, the decline in soil organic C mineralization from combined saltwater intrusion and prolonged inundation was not significant, but results suggest SLR could increase this soil’s susceptibility to peat collapse and accelerate nutrient and DOC export to adjacent Florida Bay.     

用SRAP标记研究根际土壤微生物的遗传多样性

将近年来新建立的分子标记技术——相关序列扩增多态性(sequence-related amplified polymorphism,SRAP)应用于土壤微生物遗传多样性研究.采用22对引物组合对20种植物根际土壤微生物进行了分析,共获得237个扩增位点,其中多态性位点221个,占93.2％.平均每对引物组合的多态位点比...     

Genomic relations among two non-mangrove and nine mangrove species of Indian Rhizophoraceae

Random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers were used to study the genomic relationship among 11 members of Indian Rhizophoraceae represented by nine true mangroves and two non-mangrove species. The AFLP and RAPD bands were scored and analyzed for genetic similarities and cluster analysis was done which separated the 11 species studied into two main groups, the true mangroves and the non-mangroves. The polymorphism observed for these markers showed a high degree of genetic diversity among the constituent taxa of the family. The phylogenetic relationship inferred from molecular marker systems supported the traditional taxonomic classification of the family Rhizophoraceae based on morphological characters at the levels of tribe, phylogeny and delimitation of genera and species, except the intra-generic classification of the genus Bruguiera and the placement of Rhizophora in the family Rhizophoraceae.     

Context-dependent changes in the resistance and resilience of soil microbes to an experimental disturbance for three primary plant chronosequences

The extrinsic factors that regulate soil microbial stability (resistance and resilience) are little understood, even though soil microbes are important drivers of ecosystem function and their stability is likely to affect soil carbon storage and plant nutrient availability. Soils were collected across three primary plant chronosequences (two in New Zealand and one in Hawaii) that differed in climate, parent material and time spans to test the following hypotheses: i) there is a tradeoff between the resistance and resilience of key soil microbial response variables, ii) this tradeoff is related to the relationship of soil microbial resistance and resilience to soil resources, iii) resources change predictably during different primary plant chronosequences, and iv) if the first three hypotheses hold and are consistent for all three chronosequences, then soil microbial resistance and resilience should change predictably across different chronosequences. Results showed that although there was a tradeoff between resistance and resilience, the role of resources in determining this was unclear. Within each chronosequence, resources that were positively related to resistance were negatively related to resilience and vice versa, consistent with our second hypothesis. However, the direction and strength of correlations between stability and soil resources depended strongly on which soil microbial response variable was measured, and the chronosequence it was measured in. Total amounts of resources often showed consistent trends with ecosystem development for each chronosequence, but the way that resource quality changed varied between chronosequences. At least partly because of the variable nature of these relationships, the trajectory of resistance and resilience during ecosystem development varied considerably across chronosequences. Thus, although consistent trends were found within each chronosequence, the relationships between the stability of different soil microbial response variables, resources and ecosystem development depended strongly on which chronosequence was considered.     

Maize growth responses to soil microbes and soil properties after fertilization with different green manures

The use of green manures in agriculture can provide nutrients, affect soil microbial communities, and be a more sustainable management practice. The activities of soil microbes can effect crop growth, but the extent of this effect on yield remains unclear. We investigated soil bacterial communities and soil properties under four different green manure fertilization regimes (Vicia villosa, common vetch, milk vetch, and radish) and determined the effects of these regimes on maize growth. Milk vetch showed the greatest potential for improving crop productivity and increased maize yield by 31.3 %. This change might be related to changes in soil microbes and soil properties. The entire soil bacterial community and physicochemical properties differed significantly among treatments, and there were significant correlations between soil bacteria, soil properties, and maize yield. In particular, abundance of the phyla Acidobacteria and Verrucomicrobia was positively correlated with maize yield, while Proteobacteria and Chloroflexi were negatively correlated with yield. These data suggest that the variation of maize yield was related to differences in soil bacteria. The results also indicate that soil pH, alkali solution nitrogen, and available potassium were the key environmental factors shaping soil bacterial communities and determining maize yields. Both soil properties and soil microbes might be useful as indicators of soil quality and potential crop yield.

     

Growth of microbes in an oil-continuous environment

The growth of microorganisms in fermentations where oil had been maintained as the continuous phase was examined to determine whether advantage could be gained from the increased solubility of oxygen in hydrocarbon. Although cell concentrations were highest in the aqueous phase of oil-continuous systems, due to the large oil fraction, productivities achieved per unit fermenter volume were generally equivalent to those obtained from water-continuous systems. With the oil-continuous emulsions, the power requirement for aeration and mixing was less, and phase reversal resulted in a threefold concentration of cells in the aqueous medium, thereby facilitating their recovery.