Distribution of Extensive nifH Gene Diversity Across Physical Soil Microenvironments

The diversity of nitrogen-fixing bacteria is well described for aquatic environments; however, terrestrial analyses remain mostly biased to rhizobial plant–microbe associations. We maximized the level of resolution for this study through the use of nucleotide sequence information extracted from a series of soil microenvironments, ranging from macroaggregates at 2000 μm to the clay fraction at <75 μm in diameter. In addition, we attempted to create an overview of the distribution of terrestrial nitrogen fixers across such microenvironments by combining culture-independent techniques with a suite of natural soil environments from uniquely different origins. Soil diazotroph diversity was analyzed phylogenetically for 600 terrestrial nifH sequences from 12 midsized clone libraries based on microenvironments of three separate soils across a global scale. Statistical analyses of nifH gene clone libraries were used to estimate coverage, establish degrees of sequence overlap, and compare cluster distributions. These analyses revealed an extensive diversity in a tropical (19 phylotypes) and an arctic soil (17 phylotypes), and moderate diversity in a temperate soil (11 phylotypes). Within each soil, comparisons across aggregate size fractions delineated nifH gene cluster shifts within populations and degrees of sequence overlap that ranged from significantly different (arctic, tropical) to significantly similar (temperate). We suggest that this is due to population separation across aggregates of different size classes, which results from differences in the temporal stability of aggregates as niches for microbial communities. This study not only provides new knowledge of the arrangement of diazotrophic communities at the soil microscale, but it also contributes to the underrepresented knowledge of soil nifH sequences in the public databases.     

Diversity of <Emphasis Type="Italic">nifH</Emphasis> gene amplified from plankton-community DNA in a shallow eutrophic lake (Lake Donghu,Wuhan, China)

Biological nitrogen fixation (BNF) is one of the major nitrogen inputs into the biosphere, and the nitrogenase iron protein (nifH) gene plays important roles in regulating the molecular nitrogen (N₂) fixation process. The nifH gene has also been extensively used to study the diversity and function of nitrogen-fixing microorganisms. In this study, we investigated the diversity of the nifH gene by culture-independent methods to analysis the planktonic nitrogen-fixing organisms in Lake Donghu, Wuhan, the largest urban lake in China. Results indicate that nifH gene sequences cloned from planktonic-community DNA showed high similarity to the uncultured cyanobacterial sequences deposited in the GenBank database. Phylogenetic analysis on the basis of the translated amino acid sequences further showed that most nifH clones were closely related to the reported cyanobacterial nifH gene sequences. Results also indicate that there are similar planktonic nitrogen-fixing organisms in the relatively independent areas of Lake Donghu, even though different regions showed a wide gradient in trophic status. These and other observations led us to believe that studies on nifH gene diversity and expression will increase our ability to understand the ecological function of target nitrogen-fixing groups in aquatic ecosystems.     

Molecular Diversity of nifH Genes from Bacteria Associated with High Arctic Dwarf Shrubs

Biological nitrogen fixation is the primary source of new N in terrestrial arctic ecosystems and is fundamental to the long-term productivity of arctic plant communities. Still, relatively little is known about the nitrogen-fixing microbes that inhabit the soils of many dominant vegetation types. Our objective was to determine which diazotrophs are associated with three common, woody, perennial plants in an arctic glacial lowland. Dryas integrifolia, Salix arctica, and Cassiope tetragona plants in soil were collected at Alexandra Fiord, Ellesmere Island, Canada. DNA was extracted from soil and root samples and a 383-bp fragment of the nifH gene amplified by the polymerase chain reaction. Cloned genotypes were screened for similarity by restriction fragment length polymorphism (RFLP) analysis. Nine primary RFLP phylotypes were identified and 42 representative genotypes selected for sequencing. Majority of sequences (33) were type I nitrogenases, whereas the remaining sequences belonged to the divergent, homologous, type IV group. Within the type I nitrogenases, nifH genes from posited members of the Firmicutes were most abundant, and occurred in root and soil samples from all three plant species. nifH genes from posited Pseudomonads were found to be more closely associated with C. tetragona, whereas nifH genes from putative alpha-Proteobacteria were more commonly associated with D. integrifolia and S. arctica. In addition, 12 clones likely representing a unique clade within the type I nitrogenases were identified. To our knowledge, this study is the first to report on the nifH diversity of arctic plant-associated soil microbes.     

Influences of dams with different levels of river connectivity on the fish community structure along a tropical river in Southeastern Brazil

The influence of three types of dams with different degrees of river connectivity on the structure of fish communities along the Paraíba do Sul River was studied: total blockage (Dam 1); partial blockage allowed by a permanent lateral channel (Dam 2); and total blockage, but with a mechanism operating in the summer for fish passage (Dam 3). The tested hypothesis is that the degree of river connectivity influences the fish community. The largest differences in fish fauna were expected between the reservoir and downriver stretch in Dam 1 with total blockage; an intermediate difference in Dam 3 with total blockage but with a fish passage; and the least difference in Dam 2 with partial blockage. Fish were caught by gill nets between January and March 2010 and between January and February 2011 (wet seasons) in two zones: the reservoir and the downriver stretch from the dam. A total of 43 fish species was recorded, including eight non‐native and two marine species. The 13 most abundant species (n > 100; frequency of occurrence >20%) occurred in all three stretches of the river. The community structure changed significantly between the reservoir and associated downriver stretch, with higher richness downriver compared to the reservoir zone. A trend for higher occurrence of migratory fishes (e.g. Pimelodus maculatus, Pimelodus fur, Leporinus copelandii and Prochilodus lineatus) was found in the downriver zone, suggesting the influence of dams on their upriver migration. The predictions were not fully matched. Although the most significant difference in the fish community structure between the reservoir and the downriver was found for Dam 1, the partial blockage in Dam 2 showed broader differences in the fish fauna than the total blockage in Dam 3 with the fish ladder, which may indicate that the latter is not a guarantee that species and genetic flux will be interchanged, since the water velocity may be a constraint to upriver fish migration.     

nifH Sequences and Nitrogen Fixation in Type I and Type II Methanotrophs

Some methane-oxidizing bacteria (methanotrophs) are known to be capable of expressing nitrogenase and utilizing N₂ as a nitrogen source. However, no sequences are available for nif genes in these strains, and the known nitrogen-fixing methanotrophs are confined mainly to a few genera. The purpose of this work was to assess the nitrogen-fixing capabilities of a variety of methanotroph strains. nifH gene fragments from four type I methanotrophs and seven type II methanotrophs were PCR amplified and sequenced. Nitrogenase activity was confirmed in selected type I and type II strains by acetylene reduction. Activities ranged from 0.4 to 3.3 nmol/min/mg of protein. Sequence analysis shows that the nifH sequences from the type I and type II strains cluster with nifH sequences from other gamma proteobacteria and alpha proteobacteria, respectively. The translated nifH sequences from three Methylomonas strains show high identity (95 to 99%) to several published translated environmental nifH sequences PCR amplified from rice roots and a freshwater lake. The translated nifH sequences from the type II strains show high identity (94 to 99%) to published translated nifH sequences from a variety of environments, including rice roots, a freshwater lake, an oligotrophic ocean, and forest soil. These results provide evidence for nitrogen fixation in a broad range of methanotrophs and suggest that nitrogen-fixing methanotrophs may be widespread and important in the nitrogen cycling of many environments.     

Diazotrophic Diversity and Distribution in the Tropical and Subtropical Atlantic Ocean

To understand the structure of marine diazotrophic communities in the tropical and subtropical Atlantic Ocean, the molecular diversity of the nifH gene was studied by nested PCR amplification using degenerate primers, followed by cloning and sequencing. Sequences of nifH genes were amplified from environmental DNA samples collected during three cruises (November-December 2000, March 2002, and October-November 2002) covering an area between 0 to 28.3°N and 56.6 to 18.5°W. A total of 170 unique sequences were recovered from 18 stations and 23 depths. Samples from the November-December 2000 cruise contained both unicellular and filamentous cyanobacterial nifH phylotypes, as well as γ-proteobacterial and cluster III sequences, so far only reported in the Pacific Ocean. In contrast, samples from the March 2002 cruise contained only phylotypes related to the uncultured group A unicellular cyanobacteria. The October-November 2002 cruise contained both filamentous and unicellular cyanobacterial and γ-proteobacterial sequences. Several sequences were identical at the nucleotide level to previously described environmental sequences from the Pacific Ocean, including group A sequences. The data suggest a community shift from filamentous cyanobacteria in surface waters to unicellular cyanobacteria and/or heterotrophic bacteria in deeper waters. With one exception, filamentous cyanobacterial nifH sequences were present within temperatures ranging between 26.5 and 30°C and where nitrate was undetectable. In contrast, nonfilamentous nifH sequences were found throughout a broader temperature range, 15 to 30°C, more often in waters with temperature of <26°C, and were sometimes recovered from waters with detectable nitrate concentrations.     

A System of Oligonucleotide Primers for the Amplification of nifH Genes of Different Taxonomic Groups of Prokaryotes

Based on the analysis of the nifH gene nucleotide sequences from GenBank, a system of primers was developed that makes it possible to obtain 370- and 470-bp PCR fragments of the nifH gene of nitrogen-fixing bacteria and archaea. The effectiveness of the proposed system for revealing the presence of nifH genes was demonstrated by PCR on the DNA isolated from nitrogen-fixing prokaryotes for which the primary structure of these genes is known and which belong to different taxonomic groups. nifH sequences of nitrogen-fixing prokaryotes of the genera Xanthobacter, Beijerinckia, and Methanosarcina, for which the capacity for nitrogen fixation was demonstrated earlier, but no data existed on the nucleotide composition of these genes, were determined and deposited in GenBank.     

Phylogenetic diversity of nitrogen-fixing bacteria in mangrove sediments assessed by PCR-denaturing gradient gel electrophoresis

Culture-independent PCR–denaturing gradient gel electrophoresis (DGGE) was employed to assess the composition of diazotroph species from the sediments of three mangrove ecosystem sites in Sanya, Hainan Island, China. A strategy of removing humic acids prior to DNA extraction was conducted, then total community DNA was extracted using the soil DNA kit successfully for nifH PCR amplification, which simplified the current procedure and resulted in good DGGE profiles. The results revealed a novel nitrogen-fixing bacterial profile and fundamental diazotrophic biodiversity in mangrove sediments, as reflected by the numerous bands present DGGE patterns. Canonical correspondence analysis (CCA) revealed that the sediments organic carbon concentration and available soil potassium accounted for a significant amount of the variability in the nitrogen-fixing bacterial community composition. The predominant DGGE bands were sequenced, yielding 31 different nifH sequences, which were used in phylogenetic reconstructions. Most sequences were from Proteobacteria, e.g. α, γ, β, δ-subdivisions, and characterized by sequences of members of genera Azotobacter, Desulfuromonas, Sphingomonas, Geobacter, Pseudomonas, Bradyrhizobium and Derxia. These results significantly expand our knowledge of the nitrogen-fixing bacterial diversity of the mangrove environment.     

A <Emphasis Type="Italic">nifH</Emphasis>-based Oligonucleotide Microarray for Functional Diagnostics of Nitrogen-fixing Microorganisms

Nitrogen fixation is an important process in biogeochemical cycles exclusively carried out by prokaryotes, mostly by an evolutionarily conserved nitrogenase protein complex, of which one of the structural genes (nifH) is highly valuable for phylogenetic and diversity analyses. We developed a nifH-based short oligonucleotide microarray (nifH diagnostic microarray) as a rapid tool to effectively monitor nitrogen-fixing diazotrophic populations in a wide range of environments. Taking account of the overwhelming predominance of environmental nifH fragments from uncultivated microorganisms in public databases, our nifH microarray is mainly based on nifH sequences from as yet unidentified prokaryotes. Standard conditions for microarray performance were determined, and criteria for the design of specific oligonucleotides were defined. A primary set of 56 oligonucleotides was validated with fluorescence-labeled single-stranded nifH targets from five reference strains, 26 environmental clones, and artificial mixtures of reference strains. The nifH microarray was applied to analyze the diversity (based on DNA) and activity (based on mRNA) of diazotrophs in roots of wild rice samples from Namibia. Results demonstrated that only a small subset of diazotrophs being present in the sample were actually fixing nitrogen actively. Our data suggest that the developed nifH microarray is a highly reproducible and semiquantitative method for mapping the variability of diazotrophic diversity, allowing rapid comparisons of the relative abundance and activity of diazotrophic prokaryotes in the environment. A further refined nifH microarray comprising of 194 oligonucleotide probes now covers more than 90% of sequences in our nifH database. Electronic Supplementary Material The following supplementary material is available on-line for this article from     

A Study of Nucleotide Sequences of nifH Genes of Some Methanotrophic Bacteria

Using a previously developed primer system, nifH gene fragments 450 nucleotides long were amplified, cloned, and sequenced for representatives of nitrogen-fixing methanotrophic bacteria of the genera Methylococcus, Methylocystis, and Methylosinus. Fragments of nifH genes were also detected and sequenced in representatives of the genera Methylomonas and Methylobacter, which were not considered diazotrophs until recently. Phylogenetic analysis revealed the remoteness of nifH gene sequences of methanotroph types I and II. At the same time, a close relationship was found between nifH of type I methanotrophs and representatives of -proteobacteria and between nifH genes of type II methanotrophs and representatives of -proteobacteria. The results obtained in this study are in good accordance with the data of phylogenetic analysis based on 16S rRNA sequence comparison with the only exception being Methylococcus capsulatus strains, whose nifH genes proved to be closely related to nifH genes of Methylocystis and Methylosinus representatives. Our findings extend the database of primary sequences of nifH genes and allow the contribution of methanotrophs to the process of nitrogen fixation to be estimated.     

海南高隆湾红树林及其近岸海域沉积物的弗兰克氏菌(Frankia)多样性分布及其与环境因子的关系

弗兰克氏菌(Frankia)因其独特高效的固氮效率而备受关注,然而目前的研究还局限于陆地生境。基于nifH基因采用高通量测序对高隆湾红树林及其近岸海域沉积物的Frankia多样性进行分析,共获得261条属于Frankia的nifH序列,共11个OTUs,序列主要分布在红树林区样品,其中以角果木和红海榄为优势树种的红树林样品中序列较多,在潮间带样品中也有少量分布,海草区样品未检测到,序列在不同生境中的分布存在较大差异。OTU818在10个站位都有分布,说明OTU818代表的Frankia类群分布比较广泛,且为红树林沉积物的优势类群。系统进化分析表明Frankia与NCBI数据库中的Frankia基因序列在系统发育树上形成不同分支。通过Network分析Frankia与其他细菌类群的共发生关系,发现Frankia与来自Verrucomicrobia、Proteobacteria、Firmicutes、Cyanobacteria的多种固氮细菌类群存在紧密联系,表明Frankia在稳定红树林固氮细菌群落结构中起着重要作用。利用典范对应分析(canonical correspondence an...     

Adult paddlefish migrations in relation to spring river conditions of the Yellowstone and Missouri rivers, Montana and North Dakota, USA

Migrations and movements of paddlefish (Polyodon spathula) into the regulated Missouri River and the largely unregulated Yellowstone River, North Dakota and Montana, USA were monitored with radio‐telemetry to assess if (i) differential discharge between the Yellowstone River and the Missouri River influenced river selection, (ii) river conditions influenced directional movements in the Yellowstone River and (iii) inter‐annual and sex‐related migration patterns existed. In 2003 and 2004, telemetered upriver migrants selected the Yellowstone River rather than the Missouri River above its confluence with the Yellowstone River 34 of 54 times (63%). Fish typically ascended the river with flows that were increasing at a greater rate or decreasing at a lesser rate than the other river. Most (70%) upriver movements occurred when discharge and suspended sediment were increasing. Most (80%) downriver movements occurred when flows and suspended sediment were decreasing. Total migration distance was greater in 2004 than in 2003 for both sexes despite greater peak discharge in 2003. Movement of pre‐spawn paddlefish into the Missouri River above its confluence with the Yellowstone River in response to attraction flows may have implications towards this stock’s reproductive success. Accordingly, these implications should be taken into account when regulating spring Missouri River discharge levels upriver at Fort Peck Dam.     

Environmental Constraints Underpin the Distribution and Phylogenetic Diversity of <Emphasis Type="Italic">nifH</Emphasis> in the Yellowstone Geothermal Complex

Biological nitrogen fixation is a keystone process in many ecosystems, providing bioavailable forms of fixed nitrogen for members of the community. In the present study, degenerate primers targeting the nitrogenase iron protein-encoding gene (nifH) were designed and employed to investigate the physical and chemical parameters that underpin the distribution and diversity of nifH as a proxy for nitrogen-fixing organisms in the geothermal springs of Yellowstone National Park (YNP), Wyoming. nifH was detected in 57 of the 64 YNP springs examined, which varied in pH from 1.90 to 9.78 and temperature from 16°C to 89°C. This suggested that the distribution of nifH in YNP is widespread and is not constrained by pH and temperature alone. Phylogenetic and statistical analysis of nifH recovered from 13 different geothermal spring environments indicated that the phylogeny exhibits evidence for both geographical and ecological structure. Model selection indicated that the phylogenetic relatedness of nifH assemblages could be best explained by the geographic distance between sampling sites. This suggests that nifH assemblages are dispersal limited with respect to the fragmented nature of the YNP geothermal spring environment. The second highest ranking explanatory variable for predicting the phylogenetic relatedness of nifH assemblages was spring water conductivity (a proxy for salinity), suggesting that salinity may constrain the distribution of nifH lineages in geographically isolated YNP spring ecosystems. In summary, these results indicate a widespread distribution of nifH in YNP springs, and suggest a role for geographical and ecological factors in constraining the distribution of nifH lineages in the YNP geothermal complex.     

Nitrogenase diversity and activity in the gastrointestinal tract of the wood-eating catfish Panaque nigrolineatus

The Amazonian catfish, Panaque nigrolineatus, consume large amounts of wood in their diets. The nitrogen-fixing community within the gastrointestinal (GI) tract of these catfish was found to include nifH phylotypes that are closely related to Clostridium sp., Alpha and Gammaproteobacteria, and sequences associated with GI tracts of lower termites. Fish fed a diet of sterilized palm wood were found to contain nifH messenger RNA within their GI tracts, displaying high sequence similarity to the nitrogen-fixing Bradyrhizobium group. Nitrogenase activity, measured by acetylene reduction assays, could be detected in freshly dissected GI tract material and also from anaerobic enrichment cultures propagated in nitrogen-free enrichment media; nifH sequences retrieved from these cultures were dominated by Klebsiella- and Clostridium-like sequences. Microscopic examination using catalyzed reporter deposition-enhanced immunofluorescence revealed high densities of nitrogenase-containing cells colonizing the woody digesta within the GI tract, as well as cells residing within the intestinal mucous layer. Our findings suggest that the P. nigrolineatus GI tract provides a suitable environment for nitrogen fixation that may facilitate production of reduced nitrogen by the resident microbial population under nitrogen limiting conditions. Whether this community is providing reduced nitrogen to the host in an active or passive manner and whether it is present in a permanent or transient relationship remains to be determined. The intake of a cellulose rich diet and the presence of a suitable environment for nitrogen fixation suggest that the GI tract microbial community may allow a unique trophic niche for P. nigrolineatus among fish.     

Analysis of the diversity of diazotrophic bacteria in peat soil by cloning of the <Emphasis Type="Italic">nifH</Emphasis> gene

The diversity of nitrogen-fixing microorganisms in the soil of an oligotrophic Sphagnum peat bog was studied by molecular cloning of fragments of the nifH gene encoding one of the main components of the nitrogenase complex. The fragments were amplified from the DNA isolated from the peat samples collected at the same site in January (library I) and November (library II), 2005. Analysis of the nifH sequence libraries revealed high diversity of diazotrophic bacteria in peat soil: the first library consisted of 237 clones and 55 unique sequence types, the second one included 171 clones and 52 sequence types. Comparison of the two clone libraries showed that the composition and population structure of the nitrogen-fixing community depended greatly on the sampling time; they shared only 11 phylotypes. The sequences of representatives of the class Alphaproteobacteria prevailed in both libraries (27% and 57% of clones in libraries I and II, respectively). Representatives of the classes Deltaproteobacteria and Chlorobea were minor components of library I (6% and 7% of clones, respectively), whereas they prevailed in library II (18% and 24% of clones, respectively). Members of the class Chloroflexi were present only in library I, while members of the classes Bacilli, Clostridia, and Methanomicrobia were present only in library II. Our studies demonstrated that, for complete evaluation of the diversity of natural nitrogen-fixing communities, nifH libraries should consist of at least 200–300 clones.     

Characterization of freshwater benthic biofilm‐forming Hydrocoryne (Cyanobacteria) isolates from Antarctica

The aims of this work were to study cyanobacterial isolates resembling the genus Hydrocoryne using a combination of morphology and phylogeny of 16S rRNA and nifH sequences and to investigate genes involved in cyanotoxin and protease inhibitor production. Four new cyanobacterial strains, isolated from biofilm samples collected from King George Island, Antarctica, were studied. In terms of morphology, these new strains share traits similar to true Anabaena morphotypes (benthic ones), whereas phylogenetic analysis of their 16S rRNA gene sequences grouped them with the sequence of the type species Hydrocoryne spongiosa (H. Schwabe ex Bornet and Flahault 1886–1888), but not with sequences of the type species from the genus Anabaena. This cluster is the sister group of Anabaena morphotypes isolated only from the Gulf of Finland. In addition, this cluster is related to two other clusters formed by sequences of Anabaena isolated from different sites. Partial nifH genes were sequenced from two strains and the phylogenetic tree revealed that the Antarctic nifH sequences clustered with sequences from Anabaena. Furthermore, two strains were tested, using PCR with specific primers, for the presence of genes involved in cyanotoxins (microcystin and saxitoxin) and protease inhibitor (aeruginosin, and cyanopeptolin). Only cyanopeptolin was amplified using PCR. These four Hydrocoryne strains are the first to be isolated and sequenced from Antarctica, which improves our knowledge on this poorly defined cyanobacterial genus.     

Vertical Distribution of Nitrogen-Fixing Phylotypes in a Meromictic,Hypersaline Lake

We investigated the diversity of nitrogenase genes in the alkaline, moderately hypersaline Mono Lake, California to determine (1) whether nitrogen-fixing (diazotrophic) populations were similar to those in other aquatic environments and (2) if there was a pattern of distribution of phylotypes that reflected redox conditions, as well as (3) to identify populations that could be important in N dynamics in this nitrogen-limited lake. Mono Lake has been meromictic for almost a decade and has steep gradients in oxygen and reduced compounds that provide a wide range of aerobic and anaerobic habitats. We amplified a fragment of the nitrogenase gene (nifH) from planktonic DNA samples collected at three depths representing oxygenated surface waters, the oxycline, and anoxic, ammonium-rich deep waters. Forty-three percent of the 90 sequences grouped in nifH Cluster I. The majority of clones (57%) grouped in Cluster III, which contains many known anaerobic bacteria. Cluster I and Cluster III sequences were retrieved at every depth indicating little vertical zonation in sequence types related to the prominent gradients in oxygen and ammonia. One group in Cluster I was found most often at every depth and accounted for 29% of all the clones. These sequences formed a subcluster that contained other environmental clones, but no cultivated representatives. No significant nitrogen fixation was detected by the ¹⁵N₂ method after 48 h of incubation of surface, oxycline, or deep waters, suggesting that pelagic diazotrophs were contributing little to nitrogen fluxes in the lake. The failure to measure any significant nitrogen fixation, despite the detection of diverse and novel nitrogenase genes throughout the water column, raises interesting questions about the ecological controls on diazotrophy in Mono Lake and the distribution of functional genes in the environment.     

Diversity of ammonia monooxygenase (amoA) genes across environmental gradients in Chesapeake Bay sediments

Chesapeake Bay, the largest estuary in North America, encompasses a wide range of nutrient loading and trophic levels from the rivers and upper Bay to the sea, providing an ideal natural environment in which to explore relationships between functional diversity, physical/chemical complexity and ecosystem function (e.g. nitrification). In this study, amoA gene fragments (encoding subunit A of the key nitrification enzyme, ammonia monooxygenase) were PCR‐amplified from DNA extracted from sediment cores collected at five stations spanning gradients of salinity, ammonium, nitrate, oxygen and organic carbon along the Bay and Choptank River, a subestuary of the Bay. Phylogenetic analysis of ～30 amoA clones from each station revealed extensive diversity within the β‐Proteobacteria group of ammonia‐oxidizing bacteria (AOB), with the vast majority of sequences falling into coherent phylogenetic clusters distinct from sequences of cultivated AOB. Over 70% of the clones fell into two major phylogenetic clusters that appear to represent novel groups of Nitrosomonas‐like and Nitrosospira‐like amoA sequences that may be specific to estuarine and marine environments. Rarefaction analysis, estimators of genetic variation and dissimilarity indices all revealed differences in the relative amoA‐based diversity and/or richness among most of the stations, with the highest diversity at the North Bay station and the lowest at the mesohaline stations. Although salinity appears to play a role, no single physical or chemical parameter entirely explains the pattern of diversity along the estuary, suggesting that a complex combination of environmental factors may shape the overall level of AOB diversity in this dynamic environment.     

Changes in Nitrogen-Fixing and Ammonia-Oxidizing Bacterial Communities in Soil of a Mixed Conifer Forest after Wildfire

This study was undertaken to examine the effects of forest fire on two important groups of N-cycling bacteria in soil, the nitrogen-fixing and ammonia-oxidizing bacteria. Sequence and terminal restriction fragment length polymorphism (T-RFLP) analysis of nifH and amoA PCR amplicons was performed on DNA samples from unburned, moderately burned, and severely burned soils of a mixed conifer forest. PCR results indicated that the soil biomass and proportion of nitrogen-fixing and ammonia-oxidizing species was less in soil from the fire-impacted sites than from the unburned sites. The number of dominant nifH sequence types was greater in fire-impacted soils, and nifH sequences that were most closely related to those from the spore-forming taxa Clostridium and Paenibacillus were more abundant in the burned soils. In T-RFLP patterns of the ammonia-oxidizing community, terminal restriction fragments (TRFs) representing amoA cluster 1, 2, or 4 Nitrosospira spp. were dominant (80 to 90%) in unburned soils, while TRFs representing amoA cluster 3A Nitrosospira spp. dominated (65 to 95%) in fire-impacted soils. The dominance of amoA cluster 3A Nitrosospira spp. sequence types was positively correlated with soil pH (5.6 to 7.5) and NH₃-N levels (0.002 to 0.976 ppm), both of which were higher in burned soils. The decreased microbial biomass and shift in nitrogen-fixing and ammonia-oxidizing communities were still evident in fire-impacted soils collected 14 months after the fire.