Recovery and phylogenetic analysis of nifH sequences from diazotrophic bacteria associated with dead aboveground biomass of Spartina alterniflora.

DNA was extracted from dry standing dead Spartina alterniflora stalks as well as dry Spartina wrack from the North Inlet (South Carolina) and Sapelo Island (Georgia) salt marshes. Partial nifH sequences were PCR amplified, the products were separated by denaturing gradient gel electrophoresis (DGGE), and the prominent DGGE bands were sequenced. Most sequences (109 of 121) clustered with those from alpha-Proteobacteria, and 4 were very similar (>99%) to that of Azospirillum brasilense. Seven sequences clustered with those from known gamma-Proteobacteria and five with those from known anaerobic diazotrophs. The diazotroph assemblages associated with dead Spartina biomass in these two salt marshes were very similar, and relatively few major lineages were represented.     

沼泽湿地互花米草植物体传输与排放甲烷特征

于各测定月的小潮日,使用悬管装置采集气样并结合气相色谱测定,对闽江河口互花米草（Spartina alterniflora）沼泽湿地互花米草植株的甲烷传输量及其主要释放部位进行了研究,另又采用静态箱法-气相色谱法测定了互花米草沼泽湿地甲烷的排放通量,以此分析互花米草植物体甲烷传输对互花米草沼泽湿地甲烷排放通量的贡献率,最后测定了互花米草植株髓腔内的甲烷浓度。结果表明,不同生长阶段的互花米草植株甲烷传输量明显不同,快速生长阶段的互花米草植株甲烷传输量最高;互花米草植株甲烷传输对互花米草沼泽湿地甲烷排放通量的贡献率介于9%-94%之间;互花米草植物体传输甲烷的主要释放部位是距地面0-20cm处,该部位对植物甲烷传输量的贡献率为50%（平均值）;髓腔内的甲烷浓度远高于大气中的甲烷浓度,且自下而上呈递减趋势。     

Estimation of the primary productivity of Spartina alterniflora using a canopy model

A comprehensive canopy productivity model was built to study the productivity of a primary salt marsh grass, Spartina alterniflora. in Georgia, USA The canopy model was unique in employing plant demographic data to reconstruct canopy profiles and dynamics, which showed many growth processes that are otherwise difficult to discern in the field By linking canopy dynamics and leaf photosynthesis, the net total primary productivity of S alterniflora m a Georgia salt marsh was estimated to be 1421, 749, and 1441 g C m^-2 yr^-1 for the tall, short, and N-fertilized short populations respectively These estimates are reasonable in terms of the physiological capacity of S alterniflora and well below the range of 3000–4200 g C m^-2 yr^-1 as reported by some recent harvest studies Our detailed analysis suggested the net total productivity of S alterniflora might be greatly overestimated in the past This is mainly because of 1) failure to consider the translocation of photosynthate between aboveground and belowground parts, and 2) possible overestimates of belowground production We estimated the net belowground production to be 872, 397, and 762 g C m^-2 yr^-1 for the tall, short, and N-fertilized populations respectively After receiving nitrogen fertilizer, the net leaf carbon fixation in the short population increased from 1489 to 2487 g C m^-2 yr^-1, and our simulation showed the contribution of elevated leaf N to this increase was small, 21%, compared with that of increased leaf area, 79% Both tall and short populations allocated ca 48-49% of their annual gross leaf carbon fixation to belowground structures Nitrogen enrichment caused more allocation to aboveground parts in the short population, mainly for increasing leaf area The canopy model assumed that there was no leaf photosynthesis under tidal submergence, but if this assumption was relaxed, then leaf carbon fixation might increase 7–13% for different S alterniflora populations Although this research focused only on a salt marsh species, our general approaches, especially the coupling of leaf physiology with the reconstructed canopies, should be applicable to the study of production processes of many other plant populations     

Succession of microbial communities during a biostimulation process as evaluated by DGGE and clone library analyses

AIMS: The objective of this study was to investigate the changes in the indigenous bacterial community structure for assessing the impact of biostimulation on spilled oil. METHODS AND RESULTS: Changes in the bacterial community structure were monitored by denaturing gradient gel electrophoresis (DGGE) and clone library methods based on 16S rRNA gene (rDNA) sequences. The results of DGGE, coupled with the use of the Shannon index and principal component analysis (PCA) and clone library analyses, were consistent. In the treated (fertilized) area, one operational taxonomic unit (OTU) became dominant during the fertilization period, and it was most closely related to Pseudomonas putida. CONCLUSIONS: The bacterial community structure in the treated area was markedly different from that in the control (non-fertilized) area during the fertilization period, but in the two areas it became similar at 14 weeks after the end of fertilization. SIGNIFICANCE AND IMPACT OF THE STUDY: The results suggest that the bacterial community structure was disrupted by the biostimulation treatment, but that it recovered immediately after the end of fertilization.     

Estimation of primary production using five different methods in a Spartina alterniflora salt marsh

The aboveground production of Spartina alterniflora in a salt marsh in Barataria Bay, Louisiana, USA was estimated using five different harvest methods: peak standing crop (PSC), Milner-Hughes, Smalley, Wiegert-Evans, and Lomnicki et al., and a non-destructive method based on measurement of stem density and longevity. Annual production estimates were 831 ± 41, 831 ± 62, 1231 ± 252, 1873 ± 147 and 1437 ± 96 g dry wt m^–2 for each method, respectively. The average longevity of individually tagged young shoots was 5.2 ± 0.2 months, equivalent to an annual turnover rate of 2.3 crops per year. Among the five methods, Wiegert-Evans and Lomnicki et al. were considered more accurate than the other three because they corrected for mortality losses between sampling times. The Lomnicki et al. method was preferred over the Wiegert-Evans method because of its greater simplicity.     

Ecological control and integral utilization of Spartina alterniflora

Spartina alterniflora Loisel (S. alterniflora) is native to the Atlantic and Gulf Coasts of North America and was introduced to China in 1979. Over the years, S. alterniflora played an important role in protecting coastal banks, accelerating sediment deposition, improving local economies, and alleviating natural disasters. As an exotic species, S. alterniflora has a very strong capability of propagation, which has caused some negative effects, such as occupying ecological niches of some seashells and blocking harbors by fast sediment deposition. As a result, ecological control of S. alterniflora in some areas has drawn wide attention from biologists and ecologists in China and abroad. For this paper, we studied the technology of topography and hydrology modification to substitute S. alterniflora with P. asutralis and reported our results in a project applying this technology. Furthermore, we studied various ways to make use of biomass of S. alterniflora and found that such ways were a good alternative to ecological control of S. alterniflora.     

A diverse bacterial community in an anoxic quinoline-degrading bioreactor determined by using pyrosequencing and clone library analysis

There is a concern of whether the structure and diversity of a microbial community can be effectively revealed by short-length pyrosequencing reads. In this study, we performed a microbial community analysis on a sample from a high-efficiency denitrifying quinoline-degrading bioreactor and compared the results generated by pyrosequencing with those generated by clone library technology. By both technologies, 16S rRNA gene analysis indicated that the bacteria in the sample were closely related to, for example, Proteobacteria, Actinobacteria, and Bacteroidetes. The sequences belonging to Rhodococcus were the most predominant, and Pseudomonas, Sphingomonas, Acidovorax, and Zoogloea were also abundant. Both methods revealed a similar overall bacterial community structure. However, the 622 pyrosequencing reads of the hypervariable V3 region of the 16S rRNA gene revealed much higher bacterial diversity than the 130 sequences from the full-length 16S rRNA gene clone library. The 92 operational taxonomic unit (OTUs) detected using pyrosequencing belonged to 45 families, whereas the 37 OTUs found in the clone library belonged to 25 families. Most sequences obtained from the clone library had equivalents in the pyrosequencing reads. However, 64 OTUs detected by pyrosequencing were not represented in the clone library. Our results demonstrate that pyrosequencing of the V3 region of the 16S rRNA gene is not only a powerful tool for discovering low-abundance bacterial populations but is also reliable for dissecting the bacterial community structure in a wastewater environment.     

互花米草生物质能利用潜力

作为外来种,互花米草(Spartina alterniflora)对入侵地的生态系统产生了较强的干扰,但同时高生物量的互花米草也是一种潜在的生物质能源.发展生物质能是充分利用互花米草资源并控制其恶性扩张的较为有效和实用的途径,具有生态和经济双重效益.本文总结了互花米草生物质能的利用潜力,其表现为时间与空间上的生物量资源优势、高效的光合作用机制与高生产力、高贮能、较高的碳水化合物、蛋白质和脂肪储量以及不占用耕地等;同时介绍了互花米草生物质能开发利用现状,并指出互花米草生物质能的开发与利用有着光明的前景.     

Isolation of endophytic diazotrophic bacteria from wetland rice

Endophytic nitrogen-fixing bacteria are believed to contribute substantial amounts of N to certain gramineous crops. We have been interested to find (a) a diazotroph(s) in rice which can aggressively and stably persist and fix nitrogen in interior tissues and (b) unique rice-diazotrophic endophyte combinations. To achieve these objectives, it has been essential to find an efficient method to surface sterilize rice tissues. The method described here consists of exposing tissues to 1% Chloramine T for 15 min followed by shaking with glass beads. It has proven very efficient since (a) surface bacterial populations on the root and culm were found to be reduced by more than 90%, (b) the number of the internal colonizers was found to be significantly higher than the number of surface bacteria, and (c) colonization of root but not subepidermal tissue by gusA-marked Herbaspirillum seropedicae Z67 bacteria was found to be virtually eliminated. Nitrogen-fixing putative endophytic populations (MPN g dry wt) in the root (7.94 × 10) and culm (2.57 × 10) on field-grown IR72 plants grown in the absence of N fertilizer was found to be significantly higher near heading stage. The corresponding total putative endophyte populations in the tissues of 25 highly diverse genotypes of rice and their relatives was found to range from 10–10and 10–10, in the roots and culms, respectively. Generally, the resident bacteria were found to be non-diazotrophic, although in isolated cases diazotrophs were found, for example in the roots and culm of IR72 rice plants, or the culm of Zizaniopsis villanensis plants. The size of populations of diazotrophic bacteria in different rice genotypes was found to be 10–10 for the roots and 10–10 for the culms, respectively. The rice genera-related plants Potamophila pariffora and Rhynchoryza subulata showed the highest levels.     

Populations of Anaerobic Phototrophic Bacteria in a Spartina alterniflora Salt Marsh

Habitat-simulating media were used with the Hungate anaerobic roll tube technique to enumerate culturable anaerobic photosynthetic bacteria in sediment, tidal waters, and Spartina alterniflora plant samples collected from the salt marsh at Sapelo Island, Ga. No phototrophs were detected in samples of creekside (low marsh) sediment or in tidal waters in creekside regions. In the high marsh region, 90% of anaerobic phototrophic bacteria occurred in the top 5 mm of sediment and none were detected below 6 mm. There was a seasonal variation, with maximal populations occurring in summer and fall (mean, 4.4 × 10⁵ phototrophs g of dry sediment⁻¹) and minimal numbers occurring in winter (mean, 3.9 × 10³ phototrophs g of dry sediment⁻¹). During winter and late spring, phototrophs had a patchy distribution over the high marsh sediment surface. In contrast, during late summer they had a random uniform distribution. Tidal water collected over high marsh sediment contained an average of 8.7 × 10² phototrophs ml⁻¹, with no significant seasonal variation. Anaerobic phototrophic bacteria were also cultured from the lower stem tissue of S. alterniflora growing in both the high (4.3 × 10⁴ phototrophs g of dry tissue⁻¹) and creekside (4.9 × 10⁴ phototrophs g of dry tissue⁻¹) marsh regions. Chromatium buderi, Chromatium vinosum, Thiospirillum sanguineum, Rhodospirillum molischianum, and Chlorobium phaeobacteroides were the predominant anaerobic phototrophic species cultured from high marsh sediment. The two Chromatium species were dominant.     

互花米草入侵对沿海湿地甲烷排放的影响

采集互花米草不同入侵年限(8、11和15年)的原状土壤,采用盆栽试验,研究了土壤有机碳含量对沿海湿地CH4排放的影响。结果表明,土壤有机碳含量随着互花米草入侵年限的增加而增加。在植物生长季,互花米草入侵15年的土壤有机碳含量为12.97g·kg-1,土壤CH4排放通量为2.94mg·m-2·h-1,显著高于入侵年限为8和11a(有机碳含量为8.11和9·16g·kg-1)的土壤,其土壤CH4排放通量分别为1.95和2.34mg·m-2·h-1。这主要是由于随着土壤有机碳含量提高,不仅为产甲烷菌提供了更多底物,同时也促进了产甲烷菌数量增加,从而导致更多CH4排放。因此,在评价互花米草入侵的综合环境效应时,需要兼顾土壤固碳能力和温室气体排放。     

Recovery and Phylogenetic Analysis of nifH Sequences from Diazotrophic Bacteria Associated with Dead Aboveground Biomass of Spartina alterniflora

DNA was extracted from dry standing dead Spartina alterniflora stalks as well as dry Spartina wrack from the North Inlet (South Carolina) and Sapelo Island (Georgia) salt marshes. Partial nifH sequences were PCR amplified, the products were separated by denaturing gradient gel electrophoresis (DGGE), and the prominent DGGE bands were sequenced. Most sequences (109 of 121) clustered with those from α-Proteobacteria, and 4 were very similar (>99%) to that of Azospirillum brasilense. Seven sequences clustered with those from known γ-Proteobacteria and five with those from known anaerobic diazotrophs. The diazotroph assemblages associated with dead Spartina biomass in these two salt marshes were very similar, and relatively few major lineages were represented.     

不同建群时间下互花米草种群生长及生物量分配

采用"空间代替时间"的方法,研究具有不同建群时间的互花米草种群生长及生物量分配特征。结果表明:种群高度生长从建群2a到16a呈下降趋势,6a和16a均显著低于2a(P0.05);密度、总生物量及地上生物量从建群2a到16a均呈下降趋势,16a显著低于2a(P0.05);地下生物量、根冠比随建群时间延长先增长后降低,但前者16a显著低于2a(P0.05);同化器官生物量不随建群时间变化,而非同化器官生物量随建群时间延长而减少,6a和16a均显著低于2a(P0.05);须根和根状茎生物量随建群时间延长先增大后减小。结果显示建群16a后种群呈衰退态势,探究其原因将有助于我国互花米草的管理与控制。     

水淹对互花米草生长及生理的影响

研究了互花米草在不同没顶水淹时间处理下,株高、叶面积等生长指标以及叶片光合速率与色素、脯氨酸、可溶性糖和蛋白质含量等生理指标变化情况。结果表明,随着水淹时间延长,米草株高和叶面积呈下降趋势,叶片光合速率下降;叶片中自由水/束缚水、叶绿素和类胡萝卜素含量、可溶性糖在不同水淹时长处理之间也存在显著差异;但可溶性蛋白质和游离脯氨酸含量在各处理间差异无显著性。     

Oxygen loss from Spartina alterniflora and its relationship to salt marsh oxygen balance

Spartina alterniflora has been reported to lose significant amounts of oxygen to its rhizosphere with potentially important effects on salt-marsh biogeochemical cycling and plant productivity. The potential significance of this oxidative pathway was evaluated using laboratory split-chamber experiments to quantify oxygen loss from intact root systems under a wide variety of pre-treatment and incubation conditions including antibiotics to inhibit microbial respiration. The aerenchyma system of S. alterniflora was found to transport O₂, N₂, Ar, and CH₄ from above-ground sources to its below-ground roots and rhizomes. While non-respiratory gases were observed to move from the lacunae to water bathing the root systems, net O₂ loss did not occur; instead oxygen present outside of the roots/rhizomes was consumed. Net oxygen loss was found when resistance to gas transport was reduced in the lacunae-rhizosphere pathway by placing the root systems in a gas phase and when plant respiration was significantly reduced. Root system respiration appeared to be the major variable in the plant oxygen balance. When root and rhizome respiration was inhibited using poisons or lowered by cooling, the oxygen deficit was greatly reduced and oxygen loss was indicated. The effect of seasonal temperature changes on root system oxygen deficit presents a possible explanation as to why Spartina produces root systems with respiration rates that cannot be supported by gas transport. Overall, while oxygen loss from individual plant roots is likely, integrating measured root system oxygen loss with geochemical data indicates that the mass amount of oxygen lost from S. alterniflora root systems is small compared to the total oxygen balance of vegetated salt marsh sediments.     

Isolation and characterization of diazotrophic bacteria from banana and pineapple plants

Banana and pineapple fruit crops are widely cultivated in tropical areas where high amounts of fertilizers are applied, principally nitrogen. Over 200 kg N.ha^-1.yr^-1 is often applied to these crops. Nevertheless, developing countries face the problem of high costs of chemical fertilizers. As already demonstrated for other tropical crops, like sugar cane, the utilization of nitrogen-fixing bacteria may support the growth of these fruit plants. In this work, we demonstrate the association of nitrogen-fixing bacteria with banana and pineapple. Samples from roots, stems, leaves and fruits of different genotypes showed the occurrence of diazotrophic bacteria, when evaluated in semi-specific semi-solid media. These isolates could be separated into seven different groups according to their morphological and physiological characteristics. Additional, phylogenetic assignments were performed with group- and species-specific oligonucleotide probes. Bacteria related to the groups of Azospirillum amazonense, Azospirillum lipoferum, Burkholderia sp. and a group similar to the genus Herbaspirillum could be detected in samples of both crops. However, Azospirillum brasilense and another two groups of Herbaspirillum-like bacteria were detected only in banana plants. Two isolates of the latter group were identified as Herbaspirillum seropedicae, whereas the other isolates may represent a new Herbaspirillum species.     

Invasion of Spartina alterniflora on Zostera japonica enhances the abundances of bacteria by absolute quantification sequencing analysis

Plant invasion can alter soil organic matter composition and indirectly impact estuary ecology; therefore, it is paramount to understand how plant invasion influences the bacterial community. Here, we present an absolute quantification 16S rRNA gene sequencing to investigate the bacterial communities that were collected from Zostera japonica and Spartina alterniflora covered areas and Z. japonica degradation areas in the Yellow River Estuary. Our data revealed that the absolute quantity of bacteria in the surface layer was significantly (p < .05) higher than that in the bottom and degradation areas. Following the invasion of S. alterniflora, the abundances of Bacteroidia, Acidimicrobiaceae, and Dehalococcoidaceaewere enriched in the S. alterniflora sediment. In addition, variations in the composition of sediment bacterial communities at the phylum level were the most intimately related to total organic carbon (TOC), and the content of heavy metals could reduce the abundance of bacteria. This study provided some information to understand the effects of S. alterniflora invasion on Z. japonica from the perspective of microbiome level.