Non-metric Multidimensional Scaling Ordination Analysis Research Articles

Diversity and Phenology of Soybean Seed Fungal Endophyte Communities in the Upper Midwest United States

Infection over time by endophytic fungi in soybean seed and pods was documented in Iowa and Wisconsin in 2018. Three reproductive stages were sampled from six cultivars, with maturity groups (MG) ranging from 1.1 to 4.7, and included 216 blemish-free pods and 1,836 healthy seeds that were heavily disinfested to remove epiphytes. Thirty-five species and 11 genera were identified from 1,799 isolates using morphological and molecular evidence. Alternaria, Diaporthe, and Fusarium were dominant. The timing of endophyte infection was documented relative to MG. The lowest number of fungi were recovered from seed at R6, and infection sharply increased at R7. The abundance of Diaporthe and Fusarium isolates differed across MG and reproductive stage; shorter MGs had more Diaporthe isolates at earlier reproductive stages than longer MGs. Fusarium counts differed across MG but did not show consistent trends with seed maturity. Alternaria counts declined as seed matured but were not affected by MG. We used nonmetric multidimensional scaling to elucidate the phenology of seed infection within the endophyte community. This method helps represent the data in a lower dimension by measuring the similarity or dissimilarity between data points, making it a useful tool for grouping similar endophyte communities. The nonmetric multidimensional scaling ordination analysis of fungal taxa within endophyte communities revealed that the dominant genera in filled green pods were highly similar. However, this similarity was not observed among different stages of seed development, indicating that each taxon had distinct modes of infecting the seeds. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

An elevation transect study of testate amoeba communities up to 4000 m a.s.l. on Mount Kinabalu, Borneo

Testate amoebae are a polyphyletic assemblage of unicellular eukaryotes with a specific shell. They occur frequently in soil and freshwater habitats all over the world, important for ecosystem functioning and useful for bio-indication. Terrestrial amoeba data from Borneo or Malaysia are rarely available. In this study, data on species composition and relative abundance were presented along a transect from 1730 m up to 4000 m above sea level from 10 elevational levels on Mt. Kinabalu, Malaysian Borneo. In total 78 morphotypes of testate amoebae were recorded. Most were small (under 100 µm) and supposedly cosmopolitan. However, Certesella certesi with limited geographical distribution and some rare taxa (e.g., Padaungiella lageniformis cordiformis, Placocista jurassica, Trinema chardezi) and two undescribed morphospecies were also observed. Presence/absence and relative abundance data of testate amoebae were associated to elevation with a pronounced change at the tree line, as revealed by non-metric multidimensional scaling ordination analysis. Our data from Southeast Asia contribute to the actual discussion on distributional patterns considering elevation gradients and biogeography of eukaryotic microbes.

WOODY SPECIES COMPOSITION AND RECRUITMENT STRUCTURES OF FOUR COMMON SPECIES IN AN ARID AND SEMI-ARID ECOSYSTEM OF ETHIOPIA

The spatial variations in woody species composition and recruitment structures are less explored in arid and semi-arid ecosystems. We aimed to fill this gap by undertaking the study on three sites which were purposively selected from Awash River Basin based on their area extent and altitudinal gradients. In each vegetation site, we laid out one transect line and on each transect 12 sample plots (each size: 50 × 50 m) were placed with 200 m intervals, resulting in 36 sample plots. Woody species composition difference among the three sites was tested using Adonis2 function. Nonmetric multidimensional scaling ordination analysis was run to visualize the species composition in relation to the vegetation sites in ordination space. The difference in species richness among the sites and the effect of altitudinal variation were tested using a generalized linear model with the Poisson family. The results showed that the species composition was different among the sites and significantly dependent on altitudinal variation (P=0.001). The species richness and number of unique species was higher at Mille site when compared with other two sites, and the alpha diversities of vegetations were reciprocally related to the magnitude of beta diversity. The recruitment structure was poor in sites where the species richness was lower, although the overall patterns vary across sites. Our overall results suggest that restoration schemes need to take onto account the recruitment structure of specific species to enhance the overall health of the vegetation ecosystems, especially in arid and semi-arid ecosystems.

Composition and structure of the marine benthic community in Terra Nova Bay, Antarctica: Responses of the benthic assemblage to disturbances.

The community structure and assemblages of marine benthic organisms were investigated in coastal areas near the Jang Bogo Antarctic Research Station in Terra Nova Bay during the 2012–2018 summer seasons. We also examined the recovery pattern of marine benthic organisms following disturbance due to the construction of the Jang Bogo Station. A total of 26 taxa were identified in the study area during the experimental period. Species number and diversity indices (richness, evenness, and diversity) were relatively low compared to data previously reported from Terra Nova Bay. Sphaerotylus antarcticus, Clavularia frankliniana, Hydractinia sp., Iridaea cordata, Fragilariopsis spp., Alcyonium antarcticum, and Metalaeospira pixelli were the dominant species in this area. Of these, the diatom Fragilariopsis spp. were the most abundant species, indicating their key role in maintaining the marine benthic community and controlling biogeochemical cycling. During the construction of the Jang Bogo Station, sediment coverage increased and diatoms declined due to the release of sediment into the coastal area. In February 2014, one month after the disturbance due to cyclone, the diatom coverage increased dramatically and thereby species number, richness index, and diversity index steadily rose from 2015 to 2018. However, non-metric multidimensional scaling ordination analysis of species similarities among sampling times showed that community structure had not completely recovered by 2018. Thus, long-term monitoring is required to elucidate the post-disturbance settlement mechanisms of marine benthic organisms at the study area in Terra Nova Bay.

Abstract P4-01-22: A blood based diagnostic/prognostic for early stage breast cancer

Abstract Purpose: Although improvements in mammographic screening, including digital mammography and 3D tomosynthesis, have occurred in recent years, the positive predictive value (PPV) of mammography remains low. Screening mammography has an average PPV for biopsy of 32.6 % (range 22.2-54). Furthermore,for women with abnormally dense breasts, mammography may be hard to interpret or may provide a false negative. Here, we report a blood diagnostic for women with breast lesions that is capable of detecting and discriminating epigenetic biomarkers associated with either invasive or more benign disease. Our approach is based on the premise that circulating lymphocytes undergo epigenetic changes upon exposure to the tumor microenvironment and these changes can be followed to track tumor progression from a non-invasive to an invasive state. We hypothesized that DCIS samples with high risk for progression would maintain a predominant epigenetic signature that would match those observed in invasive disease, while those DCIS samples considered to have low risk or benign disease would resemble controls. To test the utility of these epigenetic biomarkers, we employed a novel diagnostic model which uses a combined machine learning approach integrated with the recombinatorial strategy of a genetic algorithm, to screen a large response space of thousands of CpG sites to identify a small set of CpG sites (< 20) with the highest combined predictive power. Methods: Blood was obtained from women with histologically confirmed DCIS (n=14), or invasive ductal carcinoma (n=10) and women with no evidence of breast lesions on mammography (n=10). PBMCs were isolated using a modified Ficoll-Paque gradient, and DNA was extracted using standard commercial kits. Epigenetic profiling of DNA was performed using a highly sensitive and quantitative analytics platform, which utilizes methylation sensitive restriction endonucleases to detect changes in methylation of CpG sites from standard NGS data. Risk of invasiveness potential was determined based on pathologic criteria. Samples were scored as low risk (Cribroform subtype, no necrosis, low mitotic index) or high risk (Comedo or solid subtype, high mitotic index, necrosis). Results: Non-metric multidimensional scaling ordination analysis of the CpG sites revealed highly distinct methylation patterns between Normal, DCIS and invasive samples. Using a Likelihood Ratio Test with defined ANOVA contrasts, over 14,000 significantly different methylated CpG sites were identified (p<0.05 after false discovery rate correction). A proprietary machine learning diagnostic model was employed to reduce this high-dimensional variable space to the most effective set of CpG sites. DCIS and invasive samples were discriminated in blinded tests (n=17) with 69% accuracy. Prognostic ability was determined in a blinded study of 10 DCIS samples in which we obtained an accuracy of 90% for risk assessment based on our pathological criteria. Conclusions: Preliminary studies show strong ability of the identified DNA methylation metrics to detect and discriminate invasive and non-invasive breast lesions. The quantitative sensitivity and selectivity of this new diagnostic/prognostic blood test will be determined in larger patient cohorts. Citation Format: Sims-Mourtada J, Arnold KM, Marsh A. A blood based diagnostic/prognostic for early stage breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-01-22.

Species Richness and Diversity in Bee Assemblages in a Fragment of Savanna (Cerrado) at Northeastern Brazil

The conservation of the fauna of bees inhabiting the Brazilian savanna is threatened due to changes in land use in the last decades. We investigated the composition, species richness and abundance of a bee assemblage in the vicinity of the Chapada Diamantina National Park. In addition, we compiled data on composition and diversity from another bee assemblage located in the same portion of the Cerrado, which was previously investigated by one of us almost 30 years ago, in order to produce a more complete panorama on beta diversity of bees in this region. We used a non-metric multidimensional scaling ordination analysis (NMDS) to compare composition of bee assemblages from diff erent types of open vegetation. We recorded 77 bee species (H’ = 2.95; J = 0.68), 42% of them were singletons. We collected slightly more than half of the species and 60% of the genera recorded in the bee assemblage studied three decades ago. H’ was signifi cantly lower in our area than in the previous study (t = 8.588, p <0.001), but equitability (J) was very similar. Several factors may contribute to these diff erences, including local diff erences in bee assemblage composition, diff erences in the probability of capturing the diff erent species (many rare species), factors affecting the sampling itself, and perhaps species loss over the three decades separating the two studies. The magnitude of species loss is difficult to assess because the two studies were not carried out exactly in the same area and there were differences in sampling time and sampling effort.

Abstract 4545: A liquid biopsy for breast cancer diagnosis

Abstract Purpose: Although ductal carcinoma in situ (DCIS) is considered a precursor to invasive breast cancer, only 30-50% of DCIS lesions progress to invasive cancers. There has been considerable debate over the treatment of DCIS, with some groups recommending frequent monitoring of this population for progression instead of aggressive treatment. This approach would require either recurrent biopsy, an unattractive option for most women, or a useful diagnostic test capable of discriminating DCIS and invasive breast cancer. Here, we report a blood diagnostic that is capable of detecting and discriminating epigenetic biomarkers in breast lesions that are more likely to become either invasive or those that are more benign. Our approach is based on the premise that circulating lymphocytes undergo epigenetic changes upon exposure to the tumor microenvironment and these changes can be followed to track tumor progression from a non-invasive to an invasive disease state. To test the utility of these epigenetic biomarkers, a novel diagnostic model utilizing a combined machine learning approach integrated with the recombinatorial strategy of a genetic algorithm, was used to screen a large response space of 1,000's of CpG sites to winnow down to a small set of 40 CpG sites with the highest combined predictive power. Methods: Blood was obtained from women with histologically confirmed DCIS (n=14), histologically confirmed invasive ductal carcinoma (n=10) or women with no evidence of breast lesions on mammography (n=10). Lymphocytes were isolated using a modified Ficoll-Paque gradient, and DNA was extracted using standard commercial kits. Epigenetic profiling of DNA was performed using a highly sensitive and quantitative analytics platform, which utilizes methylation sensitive restriction endonucleases to detect changes in methylation of CpG sites from standard NGS data.Results: Non-metric multidimensional scaling ordination analysis of the CpG sites revealed highly distinct methylation patterns between Normal, DCIS and invasive samples. Using a Likelihood Ratio Test with defined ANOVA contrasts, over 14,000 significantly different methylated CpG sites were identified (p<0.05 after false discovery rate correction). A proprietary machine learning diagnostic model was employed to reduce this high-dimensional variable space to the most effective set of CpG sites. DCIS and invasive samples were discriminated in blinded tests (n=17) with 69% accuracy. Conclusions: Preliminary studies show strong ability of the identified DNA methylation metrics to detect and discriminate invasive and non-invasive breast lesions. The quantitative sensitivity and selectivity of this new diagnostic/prognostic blood test will be determined in larger patient cohorts. Citation Format: Jennifer Sims-Mourtada, Kimberly M. Arnold, Adam Marsh. A liquid biopsy for breast cancer diagnosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4545.

Abstract 3369: Epigenetic DNA methylation profiling of triple negative breast cancer: a quantitative NGS approach

Abstract Triple negative breast cancer (TNBC) is an aggressive disease with a high degree of genomic instability. TNBC patients have poor prognosis and the risk of metastasis and death is increased for women who relapse within four years of treatment compared to other breast cancer subtypes. Currently, there are no reliable prognostic markers to identify which population is at risk for early relapse and the molecular mechanism for disease recurrence is not well understood. Epigenetic changes, especially DNA methylation, are common in breast cancer and have been found to be associated with increased metastatic capability. Therefore, the methylation states of genes in TNBC tumors compared to non-tumor breast tissue was examined in order to identify potential biomarkers and therapeutic targets in TNBC. Matched tumor and adjacent non-tumor tissue from patients with TNBC were obtained following surgical resection and genomic DNA was extracted. Epigenetic profiling of TNBC tumors and non-tumor tissue was performed using a highly sensitive and quantitative analytics platform, which utilizes methylation sensitive restriction endonucleases to detect changes in methylation of CpG sites. Millions of CpG sites exist within the human genome and many of these are altered with tumor formation and progression, therefore, changes in methylation profiles of CpG sites may be useful as a diagnostic and/or prognostic biomarker in TNBC patients. Non-metric multidimensional scaling ordination analysis of the CpG sites revealed highly distinct methylation patterns between tumor and non-tumor tissue. Approximately 326 sites had a significant methylation score difference (p&lt0.0025) between TNBC tumor and non-tumor tissue, with most of the CpG sites having greater than 2-fold change in methylation status. Analysis of functional gene classes using KEGG classifiers revealed a significant change in methylation patterns of genes involved in response to infections and other immune related functions. Additionally, the top ten genes with hyper- or hypomethylated sites within TNBC tumors when compared to non-tumor tissue were identified. Interestingly, Gli-1 was one of the top hypomethylated genes. Gli-1 has been shown in our lab and others to have significance in chemoresistance and recurrence in TNBC patients. Immunohistochemical analysis of TNBC tumors revealed Gli-1 overexpression in TNBC tumors compared to non-tumor tissue. Expression levels of Gli-1 in TNBC tumors correlated with stage (p&lt0.001) and recurrence free (p&lt0.0213) and overall survival (p&lt0.017). Thus, analysis of CpG methylated sites in TNBC tumors and non-tumor tissue revealed differences in epigenetic profiles allowing for distinction between tumor and non-tumor tissue. Genes in TNBC tumors with significant changes in methylation status may be potential candidate genes that serve as a diagnostic or prognostic biomarker for TNBC. Citation Format: Kimberly M. Arnold, Adam G. Marsh, Jennifer Sims-Mourtada. Epigenetic DNA methylation profiling of triple negative breast cancer: a quantitative NGS approach [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3369. doi:10.1158/1538-7445.AM2017-3369

Environmental drivers of freshwater macrophyte diversity and community composition in calcareous warm-water rivers of America and Africa

This study assessed the hypothesis that spatial and environmental drivers of river macrophyte diversity and community composition differ in relative importance in calcareous river systems located in warm regions of America versus Africa. We collected aquatic vegetation and spatio-environmental data, during 2006–11, from >200 hardwater rivers, and associated floodplain waterbodies, located up to 30° north or south of the Equator, in Mexico, Trinidad, Brazil, Argentina, U.S.A. (Florida), South Africa, Botswana and Zambia. Species rarefaction procedures were used to assess the impacts of differing sampling effort in the two continents upon estimation of γ-diversity (“species pool”). We then used a cluster analysis approach (two-way indicator species analysis: TWINSPAN) to classify samples into groups based upon species composition. Variation in species richness, community composition and six spatial and environmental variables, among samples making up these groups, were compared using ANOVA and Kruskal–Wallis procedures. Regression trees and redundancy analysis were used to infer the relative importance of spatial and environmental drivers in explaining variation in local species richness and species community composition between the two continents. Sorensen's index (Cs) was calculated to estimate species turnover (β-diversity) between African and American samples. In total, 378 macrophyte taxa were recorded, with no significant difference in mean macrophyte α-diversity between African and American sites, but with evidence for high species turnover between the two continents (Cs = 0.17). Rarefaction analysis confirmed the existence of a larger macrophyte species pool in the hardwater rivers sampled in Africa compared to America. TWINSPAN classification identified seven sample end-groups, only one of which contained a mix of sites from both continents. PERMANOVA and non-metric multidimensional scaling ordination analysis confirmed significant differences in community composition present in these sample-groups. There were substantial differences between the sample-groups for α-diversity, and for spatial and environmental variables. The high species turnover between Africa and America may be accounted for by geographical segregation, along with differences in aquatic habitat characteristics, and varying long-distance dispersal capacities of individual species. The relative importance of spatial and physicochemical drivers (latitude, pH, altitude, alkalinity and electrical conductivity but not flow) differed between the continents in influencing variation in both macrophyte diversity and community composition. Latitude was a significant, although nonlinear and rather complex, spatial driver of macrophyte α-diversity in both American and African hardwater rivers. Water chemistry variables varied in relative importance as drivers of macrophyte α-diversity for African and American sites individually, and for all sites combined, but pH and/or electrical conductivity were more important than alkalinity in each case. In all three cases, altitude was consistently the third most important driver of α-diversity. Spatial and environmental variables played important roles in structuring macrophyte community composition in warm-water calcareous rivers in both America and Africa, with latitude being the strongest individual driver. Thus, this spatial variable, which is a surrogate for numerous enviro-climatic variables, appears to be of importance in determining macrophyte distributions at large spatial scales, for the ecosystem type examined here.

Patterns of tree composition in the southern cone of South America and its relevance to the biogeographic regionalization

The biogeographic history of southern South America has led to a markedly distinct flora within the frame of the Neotropics, which is also particularly heterogeneous in terms of its eco-geographic distribution. This environmental complexity is at the base of the many and controversial classification systems that have been proposed for the vegetation of the so-called Cono Sur region (Paraguay, Chile, Argentina, Uruguay and parts of Brazil and Bolivia). In this study, we aimed to assess the floristic consistency of the main vegetation types that inhabit the region. Our dataset consisted of 116,130 occurrence records of 3662 species of shrubs and trees in 781 sampling sites spread over six countries and eight phytogeographic domains: Atlantic Forest, Pampa, Gran Chaco, Patagonia, Southern Andean, Mediterranean Chile, Temperate Pacific, and Pacific Islands. We performed a cluster analysis and nonmetric multidimensional scaling ordination analysis of this dataset followed by multi-response permutation procedures and permutational multivariate analysis of variance and taxonomic distinction index and indicator species. The greater differentiation took place among the phytogeographic domains and leaf flush regimes (evergreen, deciduous, and semideciduous) though there was also a remarkable latitudinal gradient. Our analyses showed that the pre-defined vegetation types were consistent in terms of woody flora composition and have a considerable number of indicators, many of which endemic. In terms of conservation prioritization, Atlantic Rain Forest therefore has importance because of its high species richness while temperate and mediterranean forests west of the Andes should not be ignored given that they show much higher endemism than would be expected given their species richness.

Species Assembly Patterns in Polynesian Ants

The islands of remote Polynesia contain ant faunas that have been largely introduced anthropogenically. I employed nonmetric multidimensional scaling ordination analyses to evaluate patterns of ant species assembly on 42 islands across remote Polynesia. Patterns on islands in the Hawaiian archipelago were distinctly separate from those of more southerly islands. Patterns on high islands were distinctly separate from those of atolls and low-lying islands. Patterns on small islets on the barrier reefs of high islands were more similar to those of distant atolls than those of the nearby high islands. Latitude and elevation were most strongly correlated with ordination axes; area and longitude were weakly correlated with ordination axes. Patterns are consistent with humanassisted dispersal through long-distance shipping as a primary vector of colonization, and with a greater diversity of habitat types with increasing island elevation. Similar results were obtained when a subset of 19 islands that had been more thoroughly surveyed was analyzed. I also examined patterns in species composition among communities (within islands) on three French Polynesian islands (Bora Bora, Huahine, and Moorea). On all three islands, sites grouped together distinctly in ordination space as a function of the dominant ant species. A substantial number of species pairs co-occurred less frequently than predicted by chance. Although interspecific competition appears to be important in structuring ant communities within islands, habitat affinities probably also play a role.

Influence of the artificial reef size configuration on transient ichthyofauna – Southeastern Brazil

To investigate how variations in the volume of artificial reefs affect the structure and composition of the transient ichthyofauna, reefball-type concrete modules were arranged at 9 m of depth along the northern coast of the state of Rio de Janeiro. The modules were arranged in three configurations, each in triplicate: (1) solitary modules (1 m3), (2) side-by-side modules (2 m3) and (3) modules forming a triangle (3 m3). The surrounding ichthyofauna were sampled in two periods of the year (dry: September 2009 and October 2010; rainy: April 2010 and April 2011) with gillnets to record the richness, species diversity, number of individuals and biomass per volume unit. The total mean values of richness, diversity, number of individuals and biomass did not differ significantly among the reef volumes. However, when these variables were analyzed per standardized volume unit, there was an increase in these variables with the increase in reef volume, considering all the transient ichthyofauna as well as the most representative families, Ariidae and Sciaenidae. A non-metric multidimensional scaling ordination analysis revealed differences in the composition of the ichthyofauna between the sampling periods, dominated by Sciaenidae (Stellifer rastrifer, Paralonchurus brasiliensis, Larimus breviceps and Cynoscion virescens) in the dry period and by Ariidae (Aspistor luniscutis) and Carcharinidae (Rhizoprionodon porosus) in the rainy period. The results suggest that the increase in module size from 1 to 3 m3 may result in slight alterations in the community descriptors, with a decrease in the relative values of richness, diversity and density per standardized volume unit. Furthermore, the effects of the seasonal flow of the Paraíba do Sul River may overlap the effects of reef configuration, mainly in the rainy period with higher flow. The implementation of several dispersed 1 m3 modules seems to be the most favorable configuration to attract transient ichthyofauna, especially Ariidae and Sciaenidae, on the northern coast of the state of Rio de Janeiro.

Ecology and biogeography of Himalayan diatoms: distribution along gradients of altitude, stream habitat and water chemistry

Himalayan streams, an important natural resource, are subject to numerous threats such as pollution and hydrological changes with deteriorating water quality in some areas. In order to develop diatom-based monitoring tools, we investigated diatom species composition at 206 sites in relation to variation in hydrochemistry, habitat characteristics (land use, shading, substrate), altitude and geographical position across a ca. 900 km east-west distance and a 4300 m altitudinal range in Nepal and north-west India. A total of 261 species were found, of which naviculoid (55), monoraphid (47), Gomphonema and fragilarioid (30), cymbelloid (26) taxa and Nitzschia (22) were most abundant. Many species were cosmopolitan, but some had restricted distributions. Of these, most were confined to the eastern Himalaya. More than one third of the species could not be identified. Richness and diversity increased in streams with higher Si concentrations and smaller substratum size, but were not correlated with altitude as a single factor. Canonical correspondence analysis and non-metric multidimensional scaling ordination analyses showed that different regions had distinct diatom assemblages. Important environmental gradients included basestatus, reflecting differences in geology, concentrations of Si (0.5-11.5 mg/L) and Na (0.2-9.0 mg/L), reflecting impacts from agriculture, and habitat, such as substratum size, land use and stream size. The importance of these factors varied in different climatic zones. Across the east-west range and altitudinal gradient hydrochemistry and habitat characteristics explained more of the variation in species composition than altitude and geographical position, but these factors were inter-correlated and their effects difficult to disentangle. Some species had restricted distributions along the altitudinal gradient, and particularly in the eastern Himalaya a change in species composition occurred most clearly at 2000 m a.s.l. Consequently, areas above and below this altitude should be considered separately when developing diatom-based monitoring methods.

Effect of nitrogen fertilization on methane oxidation, abundance, community structure, and gene expression of methanotrophs in the rice rhizosphere

Nitrogen, one of the limiting factors for the yield of rice, can also have an important function in methane oxidation, thus affecting its global budget. Rice microcosms, planted in the greenhouse, were treated with the N-fertilizers urea (UPK) and ammonium sulfate (APK) or were only treated with phosphorous and potassium (PK). Methane oxidation rates in PK and UPK treatments were similar during most of the rice-growing season, revealing no effect of urea. However, ammonium sulfate strongly suppressed methanogenesis providing an unfavorable environment for methanotrophs in APK treatment. Roots and rhizospheric soil samples, collected from six different growth stages of the rice plant, were analyzed by terminal restriction fragment length polymorphism (T-RFLP) of the pmoA gene. Assignment of abundant T-RFs to cloned pmoA sequences indicated that the populations on roots were dominated by type-I methanotrophs, whereas the populations in rhizospheric soil were dominated by type-II methanotrophs irrespectively of growth stages and fertilizer treatments. Non-metric multidimensional scaling ordination analysis of T-RFLP profiles revealed that the methanotrophic community was significantly (P<0.001) affected by the different fertilizer treatments; however, the effect was stronger on the roots than in the rhizospheric soil. Contrary to pmoA gene-based analysis, pmoA transcript-based T-RFLP/cloning/sequencing analysis in rhizospheric soil showed type I as the predominant methanotrophs in both PK and UPK treatments. Collectively, our study showed that type-I methanotrophs were dominant and probably active in rhizospheric soil throughout the season irrespective of nitrogen fertilizer used, whereas type-II methanotrophs were relatively more dominant under unfavorable conditions, such as in APK treatment.

Human Gut Bacterial Communities Are Altered by Addition of Cruciferous Vegetables to a Controlled Fruit- and Vegetable-Free Diet1–

In the human gut, commensal bacteria metabolize food components that typically serve as energy sources. These components have the potential to influence gut bacterial community composition. Cruciferous vegetables, such as broccoli and cabbage, contain distinctive compounds that can be utilized by gut bacteria. For example, glucosinolates can be hydrolyzed by certain bacteria, and dietary fibers can be fermented by a range of species. We hypothesized that cruciferous vegetable consumption would alter growth of certain bacteria, thereby altering bacterial community composition. We tested this hypothesis in a randomized, crossover, controlled feeding study. Fecal samples were collected from 17 participants at the end of 2 14-d intake periods: a low-phytochemical, low-fiber basal diet (i.e. refined grains without fruits or vegetables) and a high (“double”) cruciferous vegetable diet [basal diet + 14 g cruciferous vegetables/(kg body weight·d)]. Fecal bacterial composition was analyzed by the terminal restriction fragment length polymorphism (tRFLP) method using the bacterial 16S ribosomal RNA gene and nucleotide sequencing. Using blocked multi-response permutation procedures analysis, we found that overall bacterial community composition differed between the 2 consumption periods (Δ = 0.603; P = 0.011). The bacterial community response to cruciferous vegetables was individual-specific, as revealed by nonmetric multidimensional scaling ordination analysis. Specific tRFLP fragments that characterized each of the diets were identified using indicator species analysis. Putative species corresponding to these fragments were identified through gene sequencing as Eubacterium hallii, Phascolarctobacterium faecium, Burkholderiales spp., Alistipes putredinis, and Eggerthella spp. In conclusion, human gut bacterial community composition was altered by cruciferous vegetable consumption, which could ultimately influence gut metabolism of bioactive food components and host exposure to these compounds.

Effect of Removal of Hesperis matronalis (Dame's Rocket) on Species Cover of Forest Understory Vegetation in NW Indiana

Exotic invasive plant species differ in their effects on indigenous vegetation as evidenced by research evaluating community response to their removal. We used a removal approach to quantify the response of a mesic woodland to the removal versus retention of an invasive plant, Hesperis matronalis (dame's rocket) from paired treatment plots over 3 y. Cover of H. matronalis did not differ between control and treatment plots prior to removal, declined in the removal plots and remained significantly lower in cover compared to the control plots. Removal did not significantly affect species richness and species diversity (evenness, Shannon and Simpson) at the plot scale, but did result in increased species richness overall in the removal plots in the last sampling year when compared to control plots. Non-metric multidimensional scaling ordination analysis indicated a significant compositional change in the spring plant composition of plots over the 3 y, reflecting an increase in exotic woody species. Exotic woody plants, especially Rosa multiflora and Euonymus alatus, increased in cover in response to H. matronalis removal. In the 3 y, neither native nor exotic forbs, nor native woody plants responded to the removal of H. matronalis in a statistically significant manner. The increasing cover of woody invasive plants in response to the removal of H. matronalis has important management implications for restoration of degraded communities.

Introduced and native ground beetle assemblages (Coleoptera: Carabidae) along a successional gradient in an urban landscape

According to the intermediate disturbance hypothesis (IDH), species diversity should be higher at sites with intermediate levels of disturbance. We tested this hypothesis using ground beetles (Coleoptera: Carabidae) collected in pitfall traps from sites that varied in time since last disturbance. This successional gradient was embedded in an urban landscape near Montreal, Quebec. We predicted that diversity in young forests and old fields would be higher than in agricultural fields and old forests. Fifty-five species (2932 individuals) were found in 2003 and 46 species (2207 individuals) in 2004. In both years, species richness was highest from traps placed in agricultural fields. We collected nine introduced species; these had higher catch rates than the native species in both years (64.8% of total catch). When introduced species were removed from the Nonmetric Multidimensional Scaling ordination analysis, the assemblages from agricultural fields were less distinct compared to those of the other habitats, suggesting the introduced fauna is important in structuring carabid assemblages from the agricultural fields. Introduced species may play a significant role in the community composition of ground beetles in urban landscapes, and their influence may be the cause of the lack of support found for the IDH.

Spatio-temporal changes in diversity and community structure of planktonic copepods in Sagami Bay, Japan

Seasonal changes in diversity and community structure of planktonic copepods at a shelf site in Sagami Bay, Japan was studied in relation to cross-shelf interaction of species components. Seasonal mesozooplankton samples were collected from the shelf station (St. M) of the north-west part of Sagami Bay from 1995 to 1997. Vertical multi-layered samples were collected near the center of Sagami Bay (St. P) in June 1996. A total 185 copepod species were identified from the two stations. We observed a clear seasonal succession in calanoid diversity and community structure at St. M from a simple shelf water community (>11 species) during spring blooming periods to highly diverse and mixed communities (ca 20–30 species) of shelf water species coupled with various Kuroshio Current species during late summer to autumn. Cluster and non-metric multidimensional scaling ordination analyses showed two distinct calanoid community groups. One group, which included samples of St. M and the surface layer of St. P, consisted of shelf water species, such as Calanus sinicus, Ctenocalanus vanus, Paracalanus spp., and Kuroshio species, such as, Canthocalanus pauper, Scolecithrix danae, etc. The other cluster was restricted to the samples collected from mid and deep layers at St. P, which consisted of meso- and bathypelagic species and Oyashio species (cold-current species, such as Neocalanus cristatus, Pseudocalanus spp., Eucalanus bungii and Metridia pacifica). In the mid and deep layers at St. P, the population of dormant copepodid stage V (CV) of Eucalanus californicus and C. sinicus were dominant. The deep CV population of C. sinicus might be ecologically discriminated from the surface and shelf water population due to their larger body length and dormant life cycle. E. californicus was also collected at the shelf site during each spring bloom period, whereas the population might descend into the mid- and deep-layers of the central bay before summer. Our results suggest that the seasonal fluctuation of community structure in the shelf water was controlled by both physical (Kuroshio Current) and biological factors, i.e., spring bloom and ontogenetic vertical migration of E. californicus. In particular, transport and diffusion processes of Kuroshio Current in Sagami Bay played a key role in controlling the shelf water calanoid community.

Benthic macrocrustacean and insect assemblages in relation to spring habitat characteristics: patterns in abundance and diversity

We studied variation in benthic macrocrustacean and insect assemblages in relation to spring habitat characteristics in six springs located in a single groundwater area in south-west Finland. We defined five habitat types in the studied springs according to water flow and benthic substrate characteristicsminerogenic brooks, organogenic brooks, helocrenes, floating moss carpets and limnocrene pools. Most studied invertebrate orders, as well as individual taxa, showed differences in relative abundances between the habitat types, but the most common taxa occurred in all springs and habitat types. The studied macroinvertebrates were most abundant in the moss carpet sites and least abundant in the pool sites, but the difference was not statistically significant. We did not observe significant differences in mean taxonomic richness per sample between habitat classes. The observed taxonomic richness in pooled samples of habitat classes was highest in moss carpet habitat and lowest in pool habitat, and the rarefied richness estimate was lowest in pool habitat. Benthic macrocrustacean and insect assemblages varied more between habitat types than between individual springs. In an Nonmetric Multidimensional Scaling ordination analysis, spring brook sites were separated from the moss carpet and pool sites, whereas helocrene sites were widely scattered among sites in other habitat classes. The strongest ecological gradients were related to water flow and the presence of minerogenic substrate, separating lentic and lotic habitats. Abundances of moss and coarse detritus accounted for most of the within-class variation. We identified several indicator species for minerogenic and organogenic brooks and for moss carpet and pool habitats, but none for the helocrenes. We found several occurrences of two crenobiont insect species considered threatened in Finland. We suggest that combined studies on macroinvertebrate and bryophyte assemblages would be a powerful approach in assessing the biodiversity of springs.

Macroalgal assemblage structure on a coral reef in Nanwan Bay in southern Taiwan

Four-season surveys of macroalgal assemblage structure on a coral reef in southern Taiwan were performed by transect investigation from October 1999 through August 2000. Species richness increased over time, and percentage cover and biomass peaked in April. Non-metric multidimensional scaling ordination analysis of species similarities between stations showed three distinct clusters corresponding to the upper reef flat, the lower reef flat and the reef slope. The macroalgal assemblage on the lower reef flat was further grouped into two clusters corresponding to the warmer months (October 1999 and August 2000) and the cooler months (January and April 2000), suggesting the macroalgal assemblage is structured primarily by zone and secondarily by season. Species richness, percentage cover, biomass, species diversity (H') and evenness (J') were highest on the lower reef flat, reflecting greater complexity in the macroalgal assemblage in this zone. However, species diversity and evenness on the lower reef flat and the reef slope did not show seasonal variations. Species diversity in the upper reef flat decreased in the warmer months due to the dominance of an unknown red alga in October 1999 and Enteromorpha linza in August 2000. The results of ANOSIM tests showed that species structure was different not only between zones but also between seasons, and the SIMPER analyses showed that, in the warmer months, Gracilaria coronopifolia , Enteromorpha linza , Laurencia spp. and Hypnea charoides were the species that separated the lower reef flat assemblage from other assemblages. In the same way, the unknown red alga (for October 1999), Enteromorpha linza (for August 2000), Halimeda spp., Mastrophora rosea and Portieria hornemannii were the species responsible for differences in structure between the upper reef flat and the reef slope. In the cooler months, the species responsible for differences in structures between the upper reef flat and the other two zones were Sargassum spp., Gracilaria coronopifolia , Enteromorpha linza and Padina australis , and those responsible for differences between the upper reef flat and the reef slope were Hypnea charoides , Halimeda spp., Mastophora rosea , Enteromorpha linza and Portieria hornemannii . The present investigation suggests that macroalgal abundance and structure on a coral reef in Nanwan Bay in southern Taiwan have marked spatial zonation and seasonal variations, and Sargassum on the lower reef flat has become the most abundant alga, as compared to 12 years ago.