Diversity,abundance and expression of nitrite reductase (nirK)-like genes in marine thaumarchaea

Ammonia-oxidizing archaea (AOA) are widespread and abundant in aquatic and terrestrial habitats and appear to have a significant impact on the global nitrogen cycle. Like the ammonia-oxidizing bacteria, AOA encode a gene homologous to copper-containing nitrite reductases (nirK), which has been studied very little to date. In this study, the diversity, abundance and expression of thaumarchaeal nirK genes from coastal and marine environments were investigated using two mutually excluding primer pairs, which amplify the nirK variants designated as AnirKa and AnirKb. Only the AnirKa variant could be detected in sediment samples from San Francisco Bay and these sequences grouped with the nirK from Candidatus Nitrosopumilus maritimus and Candidatus Nitrosoarchaeum limnia. The two nirK variants had contrasting distributions in the water column in Monterey Bay and the California Current. AnirKa was more abundant in the epi- to mesopelagic Monterey Bay water column, whereas AnirKb was more abundant in the meso- to bathypelagic California Current water. The abundance and community composition of AnirKb, but not AnirKa, followed that of thaumarchaeal amoA, suggesting that either AnirKa is not exclusively associated with AOA or that commonly used amoA primers may be missing a significant fraction of AOA diversity in the epipelagic. Interestingly, thaumarchaeal nirK was expressed 10–100-fold more than amoA in Monterey Bay. Overall, this study provides valuable new insights into the distribution, diversity, abundance and expression of this alternative molecular marker for AOA in the ocean.     

Factors Affecting Population Trends of Plant-Parasitic Nematodes on Rangeland Grasses

The effects of environmental conditions on population trends of plant-parasitic nematodes were studied in experimental plots of five wheatgrasses in the western Utah desert. In a 3-year (1984-86) field study, soil water and temperature affected the population trends of the ectoparasites, Tylenchorhynchus acutoides and Xiphinema americanum, and the migratory endoparasite, Pratylenchus neglectus, on Fairway crested wheatgrass, Agropyron cristatum; ''Hycrest'' crested wheatgrass, A. cristatum X A. desertorura; ''Rosana'' western wheatgrass, Pascopyrum smithii; ''Oahe'' intermediate wheatgrass, Thinopyrum intermedium; and RS-1 hybrid (Elytrigia repens X Pseudoroegneria spicata). The largest soil populations of these nematode species were collected in 1984 under good plant-growth conditions. A reduction in nematode populations occurred in 1985 and 1986, possibly because of low soil-water conditions. There was a positive relationship between high soil water and maximum population densities of T. acutoides in the spring and fall of 1984, and between low soil water and minimum population densities of the nematode in 1985 and 1986. Pratylenchus neglectus populations were affected by soil water, although to a lesser degree than the ectoparasitic nematodes. Population densities of the three nematode species were significantly lower in the drier years of 1985 and 1986 than in 1984. Nematode populations were greater at the lower soil depths in the fall than in the spring or summer.     

Dynamics of Concomitant Field Populations of Hoplolaimus columbus and Meloidogyne incognita

From the fall of 1968 through the summer of 1973, a Georgia cotton field with a lengthy history of the Cotton Stunt Disease Complex was sampled for the presence of plant parasitic nematodes. Although Meloidogyne incognita was recovered on all sampling dates, concomitant populations of Hoplolaimus columbus were not recovered until the spring of 1970. During the succeeding four growing seasons, the population density and horizontal distribution of H. columbus increased, and H. columbus replaced M. incognita as the predominant phytopathogenie species. A second Georgia cotton field containing concomitant populations of H. columbus and M. incognita was observed from the fall of 1971 through the summer of 1973. In this case the horizontal distribution of both species remained relatively constant and the population density of H. columbus increased steadily. In both locations, the presence of either H. columbus or M. incognita significantly inhibited the presence of the concomitant species. In general, however, the initial spring or final fall population densities of H. columbus or M. incognita had no significant influence on the population density of the concomitant species, The data are also discussed in relation to the biological significance of H. columbus in the southeastern coastal plain.     

An experimental test of the effects of variation in recruitment intensity on intertidal community composition

The rocky intertidal has been a model system for experimentally testing hypotheses regarding the factors that structure natural communities. Many ecologists have proposed that changes in the intensity of recruitment of individuals into a community should influence community structure. Past work investigating this hypothesis has primarily been surveys of recruitment and community structure across large spatial scales. Surprisingly, no researchers to date have manipulated recruitment into a rocky intertidal community to assess the response of interactions of the whole community to variation in recruitment intensity. We manipulated the densities of Balanus glandula and Chthamalus spp. recruits across a four-fold difference at two sites spanning the Monterey Bay, California, USA, to experimentally test if differences in recruitment intensity influenced initial changes in community composition and if these changes persisted through time. The results of this work indicate that differences in recruitment influence community composition initially, but that these changes can be short-lived.     

Relationship of Temporal and Spatial Variabilities of Ammonia-Oxidizing Bacteria to Nitrification Rates in Monterey Bay, California

Temporal and spatial dynamics of ammonia-oxidizing bacteria (AOB) were examined using genes encoding 16S rRNA and ammonia monooxygenase subunit A (AmoA) in Monterey Bay, Calif. Samples were collected from three depths in the water column on four dates at one mid-bay station. Diversity estimators for the two genes showed a strong positive correlation, indicating that overlapping bacterial populations had been sampled by both sets of clone libraries. Some samples that were separated by only 15 m in depth had less genetic similarity than samples that were collected from the same depth months apart. Clone libraries from the Monterey Bay AOB community were dominated by Nitrosospira-like sequences and clearly differentiated from the adjacent AOB community in Elkhorn Slough. Many Monterey Bay clones clustered with previously identified 16S rRNA and amoA groups composed entirely of marine sequences, supporting the hypothesis that these groups are specific to the marine environment and are dominant marine AOB. In addition, novel, phylogenetically distinct groups of AOB sequences were identified and compared to sequences in the database. Only one cluster of gammaproteobacterial AOB was detected using 16S rRNA genes. Although significant genetic variation was detected in AOB populations from both vertical and temporal samples, no significant correlation was detected between diversity and environmental variables or the rate of nitrification.     

Novel lineages of Prochlorococcus and Synechococcus in the global oceans

Picocyanobacteria represented by Prochlorococcus and Synechococcus have an important role in oceanic carbon fixation and nutrient cycling. In this study, we compared the community composition of picocyanobacteria from diverse marine ecosystems ranging from estuary to open oceans, tropical to polar oceans and surface to deep water, based on the sequences of 16S-23S rRNA internal transcribed spacer (ITS). A total of 1339 ITS sequences recovered from 20 samples unveiled diverse and several previously unknown clades of Prochlorococcus and Synechococcus. Six high-light (HL)-adapted Prochlorococcus clades were identified, among which clade HLVI had not been described previously. Prochlorococcus clades HLIII, HLIV and HLV, detected in the Equatorial Pacific samples, could be related to the HNLC clades recently found in the high-nutrient, low-chlorophyll (HNLC), iron-depleted tropical oceans. At least four novel Synechococcus clades (out of six clades in total) in subcluster 5.3 were found in subtropical open oceans and the South China Sea. A niche partitioning with depth was observed in the Synechococcus subcluster 5.3. Members of Synechococcus subcluster 5.2 were dominant in the high-latitude waters (northern Bering Sea and Chukchi Sea), suggesting a possible cold-adaptation of some marine Synechococcus in this subcluster. A distinct shift of the picocyanobacterial community was observed from the Bering Sea to the Chukchi Sea, which reflected the change of water temperature. Our study demonstrates that oceanic systems contain a large pool of diverse picocyanobacteria, and further suggest that new genotypes or ecotypes of picocyanobacteria will continue to emerge, as microbial consortia are explored with advanced sequencing technology.     

Population Development of Pasteuria penetrans on Meloidogyne arenaria

A microplot study on the influence of cropping sequences with peanut in summer and bare fallowed or cover crops of rye or vetch in winter on the population development of Pasteuria penetrans was initiated in the spring of 1987. The number of spores of P. penetrans attached per second-stage juvenile of Meloidogyne arenaria race 1 increased from 0.11 in the fall of 1987 to 7.6, 8.6, and 3.6 in the fall of 1989 in the rye, vetch, and fallowed plots, respectively. Higher (P ≤ 0.05) levels of P. penetrans occurred in the rye and vetch plots than in fallowed plots. No influence of P. penetrans on peanut, rye, or vetch yield was observed in 1987 and 1988, but in 1989 peanut yield was 64% higher (P ≤ 0.05) in plots infested with P. penetrans than in plots without P. penetrans. Numbers of M. arenaria in plots without P. penetrans were influenced by the cropping sequences in the spring of 1988 and 1989 but not in the fall following the peanut crop. In the spring the plots with rye had the lowest nematode numbers in either year (P ≤ 0.05). Nematode numbers were lower (P ≤ 0.05) in plots with P. penetrans than in plots without P. penetrans in the spring of 1989 (vetch) and the fall of 1989 (rye, vetch, and fallowed).     

Fortnightly periodicity in the abundance of diatom and dinoflagellate taxa at a coastal study site

From 3 July to 15 September 2000, plankton samples were collected roughly every 2 days at three stations within 1.5 km from shore at Sunset Bay, OR. In these samples we enumerated Coscinodiscus-like diatoms, Protoperidinium spp., and the potentially toxic phytoplankter, Pseudo-nitzschia spp. Using time series analysis, the abundance of these phytoplankters was compared to wind stress, tidal range, and sea surface temperature (SST). SST was significantly cross-correlated with wind stress (lower SST occurred during upwelling favorable winds) and maximum daily tidal range (cold and warm anomalies in SST occurred around the neap and spring tides, respectively). We found no significant cross-correlations between wind stress (upwelling vs. downwelling winds) and the abundance of any of the taxa. Significant cross-correlations were found between phytoplankton abundances and the maximum daily tidal range (peak concentrations occurred between the neap and spring tides) and SST (peak concentrations occurred during periods of warmer SST). We hypothesize that this pattern of abundance may be caused by shoreward transport of offshore phytoplankton populations by internal tidal waves.     

Alternative pathways for phosphonate metabolism in thermophilic cyanobacteria from microbial mats

Synechococcus sp. represents an ecologically diverse group of cyanobacteria found in numerous environments, including hot-spring microbial mats, where they are spatially distributed along thermal, light and oxygen gradients. These thermophiles engage in photosynthesis and aerobic respiration during the day, but switch to fermentative metabolism and nitrogen fixation at night. The genome of Synechococcus OS-B′, isolated from Octopus Spring (Yellowstone National Park) contains a phn gene cluster encoding a phosphonate (Phn) transporter and a C–P lyase. A closely related isolate, Synechococcus OS-A, lacks this cluster, but contains genes encoding putative phosphonatases (Phnases) that appear to be active only in the presence of the Phn substrate. Both isolates grow well on several different Phns as a sole phosphorus (P) source. Interestingly, Synechococcus OS-B′ can use the organic carbon backbones of Phns for heterotrophic growth in the dark, whereas in the light this strain releases organic carbon from Phn as ethane or methane (depending on the specific Phn available); Synechococcus OS-A has neither of these capabilities. These differences in metabolic strategies for assimilating the P and C of Phn by two closely related Synechococcus spp. are suggestive of niche-specific constraints in the evolution of nutrient assimilation pathways and syntrophic relationships among the microbial populations of the hot-spring mats. Thus, it is critical to evaluate levels of various P sources, including Phn, in thermally active habitats and the potential importance of these compounds in the biogeochemical cycling of P and C (some Phn compounds also contain N) in diverse terrestrial environments.     

Population Dynamics of Pratylenchus penetrans,Paratylenchus sp., and Criconemella xenoplax on Western Oregon Peppermint

Endoparasitic nematode populations are usually measured separately for soil and roots without a determination of the quantitative relation between soil and root population components. In this study, Pratylenchus penetrans populations in peppermint soil, roots, and rhizomes were expressed as the density within a standardized core consisting of 500 g dry soil plus the roots and rhizomes contained therein. Populations of Paratylenchus sp. and Criconemella xenoplax in 500 g dry soil were also determined, thus measuring the total plant-parasitic nematode population associated with the plant. Mean wet root weight per standard core peaked in spring and again in late summer and was lowest early in the growing season and in early fall. Pratylenchus penetrans populations peaked 4 to 6 weeks after root weight peaks. The percentage of the total population in roots reached 70% to 90% in early April, decreased to 20% to 40% in August, and returned to higher percentages during the winter. Rhizomes never contained more than a minor proportion of the population. Mean Paratylenchus sp. populations increased through spring and peaked in late August. Mean C. xenoplax populations fluctuated, peaking in August or September. Populations of all parasitic species were lowest during winter. Evaluation using the standard core method permits assessment of the total P. penetrans population associated with the plant and of changes in root weight as well as the seasonal distribution of P. penetrans.     

Colored Mulches Affect Yield of Fresh-market Tomato Infected with Meloidogyne incognita

The effects of different-colored polyethylene mulches on the quantity and spectra of reflected light, earliness of fruit set, fruit yield and quality, and root-knot disease were studied in field-grown, staked tomato (Lycopersicon esculentum). White mulch reflected more photosynthetic light and a lower far-red-to-red ratio than red mulch, whereas black mulch reflected less than 5 percent of any color. Soil temperatures and fruit yields were recorded for tomato plants inoculated with Meloidogyne incognita race 3 at initial populations of 0, 1,000, 10,000, 50,000, or 100,000 eggs/plant and grown over black, white, or red plastic mulch in both spring and fall. Soil temperatures were lower under white mulch than under red or black mulch. Tomato yields declined as inoculum level increased. Plants grown over red mulch in the spring and inoculated with 50,000 eggs of M. incognita had greater early marketable yields than similarly inoculated plants grown over black or white mulch. Tomato plants inoculated with 100,000 eggs and grown over white mulch or red mulch in the spring had greater total yields per plot than similar plants grown over black mulch (7.39 kg and 7.71 kg vs. 3.65 kg, respectively).     

Identification and Enumeration of Marine Chroococcoid Cyanobacteria by Immunofluorescence

We used an indirect immunofluorescence technique to permit the identification and enumeration of individual or closely related strains of chroococcoid cyanobacteria of the general Synechococcus and Synechocystis in natural seawater samples. Antisera directed against each of five strains (two phycoerythrin-containing Synechococcus strains, two phycocyanin-containing Synechococcus strains, and one Synechocystis strain) were produced and tested for cross-reactions with cultures of a variety of cyanobacteria and representatives of other algae and bacteria. Each antiserum was relatively specific. The observed cross-reactions occurred between strains that were isolated from similar oceanic environments. We were able, therefore, to apply this technique to field samples. Preliminary results for April to December 1982 in Great South Bay, New York, show that Synechocystis populations are present only during spring and summer, phycocyanin-containing Synechococcus strains are only a minor component in the spring and summer, and phycoerythrin-containing Synechococcus populations become significant in summer and remain so until late fall or winter.     

Population Characteristics and Dosage Trajectory Analysis for Mesocriconema xenoplax in California Prunus Orchards

The Mesocriconema xenoplax population increased exponentially in a newly planted peach orchard. The rate of increase was greater on Nemaguard than on Lovell rootstock and was reduced by postplant nematicides. Population levels were more stable in an established almond orchard on Nemaguard rootstock. All life stages of the nematode were present year round; lower ratios of juveniles to adults in summer suggested adverse effects of temperature and dry soil. Also in summer, there was a smaller proportion of the population in the upper 30 cm of soil than at greater depths. Nematode dosage, average nematode density multiplied by accumulated degree-days (physiological time) of the sampling interval, was useful in quantifying nematode stress on trees and as an indicator of the nematode management effectiveness. The annual trajectory of the nematode dosage could be determined by two samplings, one in spring and one in fall. A nematode predator, the parasitic fungus Hirsutella rhossiliensis, did not regulate ring nematode populations in the newly planted orchard; a recovery period was necessary for increase in the prevalence of parasitism.     

Age Structure and Community Diversity of Nematodes Associated with Maize in Iowa Sandy Soils

Age structure of nematode populations around maize growing in sandy soils in Iowa was studied at soil depths of 0-15and 15-30 cm for 2 years. Numbers of Longidorus breviannulatus were generally greater at 0-15 cm than at 15-30 cm deep until mid to late season. The decline in numbers of females as the season progressed indicates that fecundity slowed and is evidence of only one generation per year. Peak populations of Pratylenchus scribneri and Xiphinema americanum occurred in late August or early September. Adults of Hoplolaimus galeatus were few in the roots but common in the soil, indicating that fertilization occurred mostly in the soil. Numbers of P. scribneri were generally greater at the lower depth, especially late in the season. Community diversity (H'') was less when nematode biomass was used instead of numbers. Numbers of H. galeatus did not decline over the winter. Numbers of L. breviannulatus, P. scribneri, and X. americanum declined significantly over the winter, but not between spring cultivation and planting.     

Genetic diversity and population structure in the tomato-like nightshades Solanum lycopersicoides and S. sitiens

Background and Aims

Two closely related, wild tomato-like nightshade species, Solanum lycopersicoides and Solanum sitiens, inhabit a small area within the Atacama Desert region of Peru and Chile. Each species possesses unique traits, including abiotic and biotic stress tolerances, and can be hybridized with cultivated tomato. Conservation and utilization of these tomato relatives would benefit from an understanding of genetic diversity and relationships within and between populations.

Methods

Levels of genetic diversity and population genetic structure were investigated by genotyping representative accessions of each species with a set of simple sequence repeat (SSR) and allozyme markers.

Key Results

As expected for self-incompatible species, populations of S. lycopersicoides and S. sitiens were relatively diverse, but contained less diversity than the wild tomato Solanum chilense, a related allogamous species native to this region. Populations of S. lycopersicoides were slightly more diverse than populations of S. sitiens according to SSRs, but the opposite trend was found with allozymes. A higher coefficient of inbreeding was noted in S. sitiens. A pattern of isolation by distance was evident in both species, consistent with the highly fragmented nature of the populations in situ. The populations of each taxon showed strong geographical structure, with evidence for three major groups, corresponding to the northern, central and southern elements of their respective distributions.

Conclusions

This information should be useful for optimizing regeneration strategies, for sampling of the populations for genes of interest, and for guiding future in situ conservation efforts.     

Microbial diversity of biofilm communities in microniches associated with the didemnid ascidian Lissoclinum patella

We assessed the microbial diversity and microenvironmental niche characteristics in the didemnid ascidian Lissoclinum patella using 16S rRNA gene sequencing, microsensor and imaging techniques. L. patella harbors three distinct microbial communities spatially separated by few millimeters of tunic tissue: (i) a biofilm on its upper surface exposed to high irradiance and O₂ levels, (ii) a cloacal cavity dominated by the prochlorophyte Prochloron spp. characterized by strong depletion of visible light and a dynamic chemical microenvironment ranging from hyperoxia in light to anoxia in darkness and (iii) a biofilm covering the underside of the animal, where light is depleted of visible wavelengths and enriched in near-infrared radiation (NIR). Variable chlorophyll fluorescence imaging demonstrated photosynthetic activity, and hyperspectral imaging revealed a diversity of photopigments in all microhabitats. Amplicon sequencing revealed the dominance of cyanobacteria in all three layers. Sequences representing the chlorophyll d containing cyanobacterium Acaryochloris marina and anoxygenic phototrophs were abundant on the underside of the ascidian in shallow waters but declined in deeper waters. This depth dependency was supported by a negative correlation between A. marina abundance and collection depth, explained by the increased attenuation of NIR as a function of water depth. The combination of microenvironmental analysis and fine-scale sampling techniques used in this investigation gives valuable first insights into the distribution, abundance and diversity of bacterial communities associated with tropical ascidians. In particular, we show that microenvironments and microbial diversity can vary significantly over scales of a few millimeters in such habitats; which is information easily lost by bulk sampling.     

The inconstant gut microbiota of Drosophila species revealed by 16S rRNA gene analysis

The gut microorganisms in some animals are reported to include a core microbiota of consistently associated bacteria that is ecologically distinctive and may have coevolved with the host. The core microbiota is promoted by positive interactions among bacteria, favoring shared persistence; its retention over evolutionary timescales is evident as congruence between host phylogeny and bacterial community composition. This study applied multiple analyses to investigate variation in the composition of gut microbiota in drosophilid flies. First, the prevalence of five previously described gut bacteria (Acetobacter and Lactobacillus species) in individual flies of 21 strains (10 Drosophila species) were determined. Most bacteria were not present in all individuals of most strains, and bacterial species pairs co-occurred in individual flies less frequently than predicted by chance, contrary to expectations of a core microbiota. A complementary pyrosequencing analysis of 16S rRNA gene amplicons from the gut microbiota of 11 Drosophila species identified 209 bacterial operational taxonomic units (OTUs), with near-saturating sampling of sequences, but none of the OTUs was common to all host species. Furthermore, in both of two independent sets of Drosophila species, the gut bacterial community composition was not congruent with host phylogeny. The final analysis identified no common OTUs across three wild and four laboratory samples of D. melanogaster. Our results yielded no consistent evidence for a core microbiota in Drosophila. We conclude that the taxonomic composition of gut microbiota varies widely within and among Drosophila populations and species. This is reminiscent of the patterns of bacterial composition in guts of some other animals, including humans.     

Effects of Tropical Rotation Crops on Meloidogyne arenaria Population Densities and Vegetable Yields in Microplots

The effects of 12 summer crop rotation treatments on population densities of Meloidogyne arenaria race 1 and on yields of subsequent spring vegetable crops were determined in microplots. The crop sequence was: (i) rotation crops during summer 1991 ; (ii) cover crop of rye (Secale cereale) during winter 1991-92; (iii) squash (Cucurbita pepo) during spring 1992; (iv) rotation crops during summer 1992; (v) rye during winter 1992-93; (vi) eggplant (Solanum melongena) during spring 1993. The 12 rotation treatments were castor (Ricinus communis), cotton (Gossypium hirsutum), velvetbean (Mucuna deeringiana), crotalaria (Crotalaria spectabilis), fallow, hairy indigo (Indigofera hirsuta), American jointvetch (Aeschynomene americana), sorghum-sudangrass (Sorghum bicolor x S. sudanense), soybean (Glycine max), horsebean (Canavalia ensiformis), sesame (Sesamum indicum), and peanut (Arachis hypogaea). Compared to peanut, the first eight rotation treatments resulted in lower (P ≤ 0.05) numbers of M. arenaria juveniles on most sampling dates. Soybean, horsebean, and sesame rotations were less effective in suppressing nematodes. Yield of squash was greater (P ≤ 0.05) following castor, cotton, velvetbean, and crotalaria than following peanut. Compared to the peanut rotation, yield of eggplant was enhanced (P ≤ 0.10) following castor, crotalaria, hairy indigo, American jointvetch, and sorghum-sudangrass. Several of these rotation crops may provide a means for depressing M. arenaria population densities on a short-term basis to enhance yields in a subsequent susceptible vegetable crop.