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.     

Analysis of a diverse assemblage of diazotrophic bacteria from Spartina alterniflora using DGGE and clone library screening

Methods to assess the diversity of the diazotroph assemblage in the rhizosphere of the salt marsh cordgrass, Spartina alterniflora were examined. The effectiveness of nifH PCR-denaturing gradient gel electrophoresis (DGGE) was compared to that of nifH clone library analysis. Seventeen DGGE gel bands were sequenced and yielded 58 nonidentical nifH sequences from a total of 67 sequences determined. A clone library constructed using the GC-clamp nifH primers that were employed in the PCR-DGGE (designated the GC-Library) yielded 83 nonidentical sequences from a total of 257 nifH sequences. A second library constructed using an alternate set of nifH primers (N-Library) yielded 83 nonidentical sequences from a total of 138 nifH sequences. Rarefaction curves for the libraries did not reach saturation, although the GC-Library curve was substantially dampened and appeared to be closer to saturation than the N-Library curve. Phylogenetic analyses showed that DGGE gel band sequencing recovered nifH sequences that were frequently sampled in the GC-Library, as well as sequences that were infrequently sampled, and provided a species composition assessment that was robust, efficient, and relatively inexpensive to obtain. Further, the DGGE method permits a large number of samples to be examined for differences in banding patterns, after which bands of interest can be sampled for sequence determination.     

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。     

Edaphic diatom communities associated with Spartina alterniflora and S. patens in New Jersey

Edaphic diatoms inhabiting the sediments beneath dwarf Spartina alterniflora Loisel. and S. patens (Ait.) Muhl. in Great Bay salt marsh, Tuckerton, New Jersey were collected from 24 September 1974 through 20 August 1975. Of the 91 taxa encountered, 8 were endemic to the dwarf S. alterniflora habitat and 42 endemic to the S. patens habitat. The edaphic diatom community associated with S. patens was comprised of a much greater number of taxa and possessed higher values for species diversity (H') and evenness (J') than the community associated with dwarf S. alterniflora. The salinity of the marsh surface showed a completely opposite trend, being greatly reduced at the S. patens habitat. A highly significant relationship (P < 0.001) between the number of diatom taxa and marsh surface salinity at the S. patens habitat was demonstrated by a least squares regression. This finding led to the conclusion that the dissimilarity in the structure of the two edaphic diatom communities was primarily due to the very low marsh surface salinities at the S. patens habitat from January through June, and that this sustained. low-salinity regime allowed a very large number of taxa to coexist only in the S. patens community. Comparison of the diatom flora of Great Bay salt marsh with that of a Delaware marsh studied previously by the author showed that 67.0% of the 91 taxa encountered in New Jersey also occur on the Delaware marsh.     

Recovery and phylogenetic analysis of novel archaeal rRNA sequences from a deep-sea deposit feeder.

In 1992, two independent reports based on small-subunit rRNA gene (SSU rDNA) cloning revealed the presence of novel Archaea among marine bacterioplankton. Here, we report the presence of further novel Archaea SSU rDNA sequences recovered from the midgut contents of a deep-sea marine holothurian. Phylogenetic analyses show that these abyssal Archaea are a paraphyletic component of a highly divergent clade that also includes some planktonic sequences. Our data confirm that this clade is a deep-branching lineage in the tree of life.     

Molecular characterization of diazotrophic and denitrifying bacteria associated with mangrove roots

An analysis of the molecular diversity of N(2) fixers and denitrifiers associated with mangrove roots was performed using terminal restriction length polymorphism (T-RFLP) of nifH (N(2) fixation) and nirS and nirK (denitrification), and the compositions and structures of these communities among three sites were compared. The number of operational taxonomic units (OTU) for nifH was higher than that for nirK or nirS at all three sites. Site 3, which had the highest organic matter and sand content in the rhizosphere sediment, as well as the lowest pore water oxygen concentration, had the highest nifH diversity. Principal component analysis of biogeochemical parameters identified soil texture, organic matter content, pore water oxygen concentration, and salinity as the main variables that differentiated the sites. Nonmetric multidimensional scaling (MDS) analyses of the T-RFLP data using the Bray-Curtis coefficient, group analyses, and pairwise comparisons between the sites clearly separated the OTU of site 3 from those of sites 1 and 2. For nirS, there were statistically significant differences in the composition of OTU among the sites, but the variability was less than for nifH. OTU defined on the basis of nirK were highly similar, and the three sites were not clearly separated on the basis of these sequences. The phylogenetic trees of nifH, nirK, and nirS showed that most of the cloned sequences were more similar to sequences from the rhizosphere isolates than to those from known strains or from other environments.     

New species of Fusarium associated with dieback of Spartina alterniflora in Atlantic salt marshes

Sudden vegetation dieback (SVD) is the loss of smooth cordgrass (Spartina alterniflora) along intertidal creeks in salt marshes of the Atlantic and Gulf states. The underlying cause of SVD remains unclear, but earlier work suggested a contributing role for Fusarium spp. in Louisiana. This report investigated whether these or other Fusarium species were associated with S. alterniflora dieback in mid- to north-Atlantic states. Isolations from seven SVD sites yielded 192 isolates of Fusarium spp., with more than 75% isolated from aboveground tissue. Most isolates (88%) fell into two undescribed morphospecies (MS) distinguished from each other by macroconidial shape, phialide ontogeny and growth rates. Pathogenicity tests on wound-inoculated S. alterniflora stems and seedling roots revealed that isolates in MS1 were more virulent than those in MS2 but no single isolate caused plant mortality. No matches to known species of Fusarium were revealed by DNA sequence queries of translation elongation factor 1-α (tef1) sequences. A phylogenetic analysis of partial sequences of three genes, β-tubulin (β-tub), calmodulin (cal) and tef1, was conducted on representative isolates from MS1 (n = 20) and MS2 (n = 18); it provided strong evidence that the MS1 isolates form a clade that represents a heretofore undescribed species, which we designate Fusarium palustre sp. nov. Isolates from the more variable MS2 clustered with the F. incarnatum-equiseti species complex as F. cf. incarnatum. Although a strong association exists between both species and declining S. alterniflora in SVD sites, neither appears to play a primary causal role in SVD. However, our findings suggest that F. palustre might play an important secondary role in the ecological disruption of the salt marshes.     

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.     

Recovery and analysis of formyltetrahydrofolate synthetase gene sequences from natural populations of acetogenic bacteria

Primers for PCR amplification of partial (1,102 of 1,680 bp) formyltetrahydrofolate synthetase (FTHFS) gene sequences were developed and tested. Partial FTHFS sequences were successfully amplified from DNA from pure cultures of known acetogens, from other FTHFS-producing organisms, from the roots of the smooth cordgrass, Spartina alterniflora, and from fresh horse manure. The amplimers recovered were cloned, their nucleotide sequences were determined, and their translated amino acid sequences were used to construct phylogenetic trees. We found that FTHFS sequences from homoacetogens formed a monophyletic cluster that did not contain sequences from nonhomoacetogens and that FTHFS sequences appear to be informative regarding major physiological features of FTHFS-producing organisms.     

Molecular phylogenetic and biogeochemical studies of sulfate-reducing bacteria in the rhizosphere of spartina alterniflora

The population composition and biogeochemistry of sulfate-reducing bacteria (SRB) in the rhizosphere of the marsh grass Spartina alterniflora was investigated over two growing seasons by molecular probing, enumerations of culturable SRB, and measurements of SO42- reduction rates and geochemical parameters. SO42- reduction was rapid in marsh sediments with rates up to 3.5 &mgr;mol ml-1 day-1. Rates increased greatly when plant growth began in April and decreased again when plants flowered in late July. Results with nucleic acid probes revealed that SRB rRNA accounted for up to 43% of the rRNA from members of the domain Bacteria in marsh sediments, with the highest percentages occurring in bacteria physically associated with root surfaces. The relative abundance (RA) of SRB rRNA in whole-sediment samples compared to that of Bacteria rRNA did not vary greatly throughout the year, despite large temporal changes in SO42- reduction activity. However, the RA of root-associated SRB did increase from <10 to >30% when plants were actively growing. rRNA from members of the family Desulfobacteriaceae comprised the majority of the SRB rRNA at 3 to 34% of Bacteria rRNA, with Desulfobulbus spp. accounting for 1 to 16%. The RA of Desulfovibrio rRNA generally comprised from <1 to 3% of the Bacteria rRNA. The highest Desulfobacteriaceae RA in whole sediments was 26% and was found in the deepest sediment samples (6 to 8 cm). Culturable SRB abundance, determined by most-probable-number analyses, was high at >10(7) ml-1. Ethanol utilizers were most abundant, followed by acetate utilizers. The high numbers of culturable SRB and the high RA of SRB rRNA compared to that of Bacteria rRNA may be due to the release of SRB substrates in plant root exudates, creating a microbial food web that circumvents fermentation.     

Diversity analysis of diazotrophic bacteria associated with the roots of tea (Camellia sinensis (L.) O. Kuntze)

The diversity elucidation by amplified ribosomal DNA restriction analysis and 16S rDNA sequencing of 96 associative diazotrophs, isolated from the feeder roots of tea on enriched nitrogen-free semisolid media, revealed the predominance of Gram-positive over Gram-negative bacteria within the Kangra valley in Himachal Pradesh, India. The Gram-positive bacteria observed belong to two taxonomic groupings; Firmicutes, including the genera Bacillus and Paenibacillus; and Actinobacteria, represented by the genus Microbacterium. The Gram-negative bacteria included alpha-Proteobacteria genera Brevundimonas, Rhizobium, and Mesorhizobium; gamma-Proteobacteria genera Pseudomonas and Stenotrophomonas; and beta-Proteobacteria genera Azospira, Burkholderia, Delftia, Herbaspirillum and Ralstonia. The low level of similarity of two isolates, with the type strains Paenibacillus xinjiangensis and Mesorhizobium albiziae, suggests the possibility of raising species novum. The bacterial strains of different phylogenetic groups exhibited distinct carbon-source utilization patterns and fatty acid methyl ester profiles. The strains differed in their nitrogenase activities with relatively high activity seen in the Gramnegative strains exhibiting the highest similarity to Azospira oryzae, Delftia lacustris and Herbaspirillum huttiense.     

Recovery of phosphorus from natural water bodies using iron-oxidizing bacteria and woody biomass

There is a global concern that phosphorus (P) resources will be depleted in the near future, but the P flux from water to land is extremely limited, whereas the reverse flux is substantial. A new method for the recovery of P from natural water bodies was proposed using iron-oxidizing bacteria and woody biomass (heartwood of conifer) as a carrier and a practical demonstration was presented. The woody carrier was immersed in water abundant in iron-oxidizing bacteria and removed 1–10 weeks later. Our results showed that the immersed carrier collected biogenic iron (Fe) oxides produced by iron-oxidizing bacteria, and contained about 0.2 mg g^?1 of P after 3 weeks; this amount was higher than that contained in some P fertile soils used for cultivating plants. The biogenic Fe oxides on the carrier acted as a source of P for plant cultivation, and they could adsorb P from P-rich solutions (10 mg L^?1 of PO₄-P). Although our study involved only a small-scale trial, the proposed method can potentially aid in the effective use of P in water and in water quality improvement if conducted on a large scale.     

冬季火烧与收割对互花米草地上部分生长与繁殖的影响

自1995年首次在崇明东滩发现互花米草(Spartinaalterniflora)以来,该外来种已在东滩扩张成为最具优势的植物之一。作为东滩常见的两种人为干扰,冬季火烧和收割可能会对互花米草的生长和繁殖有一定的促进作用,并可能进一步促进互花米草的入侵。因此,作者选择崇明东滩为实验地点,探讨冬季一次性火烧和收割以及相对高程对互花米草生长与繁殖的影响。结果表明:冬季火烧与收割能显著提高互花米草的植株密度和结穗率,显著降低其植株基部直径,即对其生长与繁殖有一定的促进作用,原因可能在于这两种干扰使其生境改变,光照条件得到改善;从Wilks’值的大小可看出,与相对高程相比,这两种干扰对互花米草生长繁殖的影响相对较小,而且这两种干扰对互花米草的影响差异不显著。上述结果表明,冬季火烧与收割将可能促进互花米草在东滩的入侵,有必要采取措施加以管理。     

Comparative and phylogenetic analysis of developmental sequences

Event pairing has been proposed for the optimization of developmental sequences (event sequences) on a given phylogenetic hypothesis (cladogram) to determine instances of sequence heterochrony. Here, we show that event pairing is faulty, leading to the optimization of impossible hypothetical ancestors, the underestimation of the lengths of the developmental sequences on the tree, and the proposition of synapomorphies that are not supported by the data. When used for phylogenetic analysis, event pairing can even produce cladograms that are inconsistent with the data. These errors are caused by the fact that event pairing treats dependent features as if they were independent. We present a new method for comparative and phylogenetic analysis of developmental sequences that does not exhibit these errors. Our method applies Search-based character optimization and treats the entire developmental sequence as a single character that is then analyzed by using an edit cost function, which specifies the transformation cost between pairs of observed and unobserved character states, and dynamic programming. In other words, the developmental sequence is directly optimized on the tree. We used event pairing as an edit cost function, but others are possible.