Marine Cyanophages Demonstrate Biogeographic Patterns throughout the Global Ocean

Myoviruses and podoviruses that infect cyanobacteria are the two major groups of marine cyanophages, but little is known of how their phylogenetic lineages are distributed in different habitats. In this study, we analyzed the phylogenetic relationships of cyanopodoviruses and cyanomyoviruses based on the existing genomes. The 28 cyanomyoviruses were classified into four clusters (I to IV), and 19 of the 20 cyanopodoviruses were classified into two clusters, MPP-A and MPP-B, with four subclusters within cluster MPP-B. These genomes were used to recruit cyanophage-like fragments from microbial and viral metagenomes to estimate the relative abundances of these cyanophage lineages. Our results showed that cyanopodoviruses and cyanomyoviruses are both abundant in various marine environments and that clusters MPP-B, II and III appear to be the most dominant lineages. Cyanopodoviruses and cluster I and IV cyanomyoviruses exhibited habitat-related variability in their relative levels of abundance, while cluster II and III cyanomyoviruses appeared to be consistently dominant in various habitats. Multivariate analyses showed that reads that mapped to Synechococcus phages and Prochlorococcus phages had distinct distribution patterns that were significantly correlated to those of Synechococcus and Prochlorococcus, respectively. The Mantel test also revealed a strong correlation between the community compositions of cyanophages and picocyanobacteria. Given that cyanomyoviruses tend to have a broad host range and some can cross-infect Synechococcus and Prochlorococcus, while cyanopodoviruses are commonly host specific, the observation that their community compositions both correlated significantly with that of picocyanobacteria was unexpected. Although cyanomyoviruses and cyanopodoviruses differ in host specificity, their biogeographic distributions are likely both constrained by the picocyanobacterial community.     

Long-Term Characterization of Free-Living and Particle-Associated Bacterial Communities in Lake Tiefwaren Reveals Distinct Seasonal Patterns

Seasonal changes in environmental conditions have a strong impact on microbial community structure and dynamics in aquatic habitats. To better elucidate the response of bacterial communities to environmental changes, we have measured a large variety of limnetic variables and investigated bacterial community composition (BCC) and dynamics over seven consecutive years between 2003 and 2009 in mesotrophic Lake Tiefwaren (NE Germany). We separated between free-living (FL, >0.2, <5.0?μm) and particle-associated (PA, >5.0?μm) bacteria to account for different bacterial lifestyles and to obtain a higher resolution of the microbial diversity. Changes in BCC were studied by DGGE based on PCR-amplified 16S rRNA gene fragments. Sequencing of DGGE bands revealed that ca. 70?% of all FL bacteria belonged to the Actinobacteria, whereas PA bacteria were dominated by Cyanobacteria (43?%). FL communities were generally less diverse and rather stable over time compared to their PA counterpart. Annual changes in reoccurring seasonal patterns of dominant freshwater bacteria were supported by statistical analyses, which revealed several significant correlations between DGGE profiles and various environmental variables, e.g. temperature and nutrients. Overall, FL bacteria were generally less affected by environmental changes than members of the PA fraction. Close association of PA bacteria with phytoplankton and zooplankton suggests a tight coupling of PA bacteria to organisms of higher trophic levels. Our results indicate substantial differences in bacterial lifestyle of pelagic freshwater bacteria, which are reflected by contrasting seasonal dynamics and relationships to a number of environmental variables.     

Nitrate-nitrogen retention in wetlands in the Mississippi River Basin

Nitrate-nitrogen retention as a result of river water diversions is compared in experimental wetland basins in Ohio for 18 wetland-years (9 years × 2 wetland basins) and a large wetland complex in Louisiana (1 wetland basin × 4 years). The Ohio wetlands had an average nitrate-nitrogen retention of 39 g-N m⁻² year⁻¹, while the Louisiana wetland had a slightly higher retention of 46 g-N m⁻² year⁻¹ for a similar loading rate area. When annual nitrate retention data from these sites are combined with 26 additional wetland-years of data from other wetland sites in the Basin Mississippi River (Ohio, Illinois, and Louisiana), a robust regression model of nitrate retention versus nitrate loading is developed. The model provides an estimate of 22,000 km² of wetland creation and restoration needed in the Mississippi River Basin to remove 40% of the nitrogen estimated to discharge into the Gulf of Mexico from the river basin. This estimated wetland restoration is 65 times the published net gain of wetlands in the entire USA over the past 10 years as enforced by the Clean Water Act and is four times the cumulative total of the USDA Wetland Reserve Program wetland protection and restoration activity for the entire USA.     

Comparison of Free-Living and Particle-Associated Bacterial Communities in the Chesapeake Bay by Stable Low-Molecular-Weight RNA Analysis

Free-living and particle-associated bacterial communities in the Chesapeake Bay estuary were analyzed and compared by using acridine orange direct counts and low-molecular-weight (LMW) RNA analysis. Samples were taken from top and bottom waters at upper- and mid-bay sites in December 1992. Free-living bacteria dominated the bacterial numbers at all sampling sites, although particle-associated bacteria increased in areas with greater particle loads. LMW RNAs (5S rRNA and tRNA) obtained directly from free-living, particle-associated, and total bacterioplankton communities were analyzed by high-resolution electrophoresis. There were distinct differences in the migration distances between LMW RNAs of free-living and particle-associated communities taken from the same site, indicating that the two communities differ in composition. In addition, LMW RNA profiles differed minimally with depth for all of the communities examined, presumably because of vertical mixing. 5S rRNAs of free-living communities from the upper- and mid-bay regions differed considerably. Particle-associated RNAs, on the other hand, were very similar, suggesting consistent environmental conditions on particles that select for similar community members. Lastly, several isolated bacteria had 5S rRNAs that were not detected in their respective extracted community 5S rRNAs, indicating that these isolated organisms were not representative of dominant members.     

Diversification Times and Biogeographic Patterns in Apiales

This study provides an overview of the historical biogeography of the major clades of Apiales based on extensive taxon sampling from all major lineages of the order, and character sampling of sequence data from the plastid rpl16 intron and trnD-trnY-trnE-trnT intergenic spacers. Divergence times were estimated in BEAST using relaxed molecular clocks and six calibration points from three families. Biogeographic reconstructions were estimated in DIVA and Lagrange using stratified and non-stratified models, addressing alternative scenarios for taxa with conflicting or poorly supported placements. Our analyses in BEAST estimated the origin of Apiales to Australasia in the Early Cretaceous (c.117 Ma). Most major clades also appear to have originated in Australasia, with the youngest family (Apiaceae) originating in the Late Cretaceous, c. 87 Ma. Diversification of the early lineages appears to be influenced by vicariance events related to the break up of Africa and Australasia (Torricelliaceae from Griseliniaceae and Apiineae), Australasia from Zealandia (e.g., Myodocarpaceae and Araliaceae), and Antarctica from South America, Australia, and possibly Africa (main lineages of Apiaceae). Long-distance dispersal appears as the likely explanation for many younger lineages within major clades, including Subantarctic pathways (e.g., Griseliniaceae and Azorelloideae), across the Pacific and Indian Ocean Basins (e.g., Pittosporaceae and Araliaceae), from Asia across Europe into the Americas (Araliaceae).     

Patterns of forest succession and impacts of flood in the Upper Mississippi River floodplain ecosystem

The widespread loss of oak-hickory forests and the impacts of flood have been major issues of ecological interest concerning forest succession in the Upper Mississippi River (UMR) floodplain. The data analysis from two comprehensive field surveys indicated that Quercus was one of the dominant genera in the UMR floodplain ecosystem prior to the 1993 flood and constituted 14% of the total number of trees and 28% of the total basal area. During the post-flood recovery period through 2006, Quercus demonstrated slower recovery rates in both the number of trees (4%) and basal area (17%). In the same period, Carya recovered greatly from the 1993 flood in terms of the number of trees (11%) and basal area (2%), compared to its minor status before the flood. Further analyses suggested that different species responded to the 1993 flood with varying tolerance and different succession strategies. In this study, the relation of flood-caused mortality rates and DBH, f_m(d), can be expressed in negative exponential functions for each species. The results of this research also indicate that the growth functions are different for each species and might also be different between pre- and post-flood time periods. These functions indicate different survival strategies and emergent properties in responding to flood impacts. This research enhances our understanding of forest succession patterns in space and time in the UPR floodplain. And such understanding might be used to predict long-term impacts of floods on UMR floodplain forest dynamics in support of management and restoration.     

River Enhancement in the Upper Mississippi River Basin: Approaches Based on River Uses, Alterations, and Management Agencies

The Upper Mississippi River is characterized by a series of locks and dams, shallow impoundments, and thousands of river channelization structures that facilitate commercial navigation between Minneapolis, Minnesota, and Cairo, Illinois. Agriculture and urban development over the past 200 years have degraded water quality and increased the rate of sediment and nutrient delivery to surface waters. River enhancement has become an important management tool employed to address causes and effects of surface water degradation and river modification in the Upper Mississippi River Basin. We report information on individual river enhancement projects and contrast project densities, goals, activities, monitoring, and cost between commercially non‐navigated and navigated rivers (Non‐navigated and Navigated Rivers, respectively). The total number of river enhancement projects collected during this effort was 62,108. Cost of all projects reporting spending between 1972 and 2006 was about US$1.6 billion. Water quality management was the most cited project goal within the basin. Other important goals in Navigated Rivers included in‐stream habitat improvement and flow modification. Most projects collected for Non‐navigated Rivers and their watersheds originated from the U.S. Department of Agriculture (USDA). The U.S. Army Corps of Engineers and the USDA were important sources for projects in Navigated Rivers. Collaborative efforts between agencies that implement projects in Non‐navigated and Navigated Rivers may be needed to more effectively address river impairment. However, the current state of data sources tracking river enhancement projects deters efficient and broad‐scale integration.     

Species Diversity,Phylogeny and Large Scale Biogeographic Patterns of the Genus Padina (Phaeophyceae,Dictyotales)

The brown algal genus Padina (Dictyotales, Phaeophyceae) is distributed worldwide in tropical and temperate seas. Global species diversity and distribution ranges, however, remain largely unknown. Species‐level diversity was reassessed using DNA‐based, algorithmic species delineation techniques based on cox3 and rbcL sequence data from 221 specimens collected worldwide. This resulted in estimates ranging from 39 to 61 putative species (ESUs), depending on the technique as well as the locus. We discuss the merits, potential pitfalls, and evolutionary and biogeographic significance of algorithmic species delineation. We unveil patterns whereby ESUs are in all but one case restricted to either the Atlantic or Indo‐Pacific Ocean. Within ocean basins we find evidence for the vast majority of ESUs to be confined to a single marine realm. Exceptions, whereby ESUs span up to three realms, are located in the Indo‐Pacific Ocean. Patterns of range‐restricted species likely arise by repeated founder events and subsequent peripatric speciation, hypothesized to dominate speciation mechanisms for coastal marine organisms in the Indo‐Pacific. Using a three‐gene (cox3, psaA and rbcL), relaxed molecular clock phylogenetic analysis we estimated divergence times, providing a historical framework to interpret biogeographic patterns.     

The impact of cropland cover on river nutrient levels in the Mississippi River Basin

Aim This study developed high‐resolution datasets of the area of maize, soybean and wheat cultivation in the United States for 1950, 1970 and 1992. The datasets were used to examine the relationship between individual crop cover and nutrient levels in rivers across the Mississippi River Basin. Location This study was conducted in the United States, with focus on the Mississippi River Basin. Methods County and state‐level estimates of the planted area of maize, soybean and wheat were integrated with a satellite‐derived pattern in total cropland to develop 5′ × 5′ resolution datasets of the fractional area of maize, soybean and wheat in the United States for 1950, 1970 and 1992. Regression analysis was used to determine the relationships between mean levels of nitrogen, phosphorous and silica in 25 rivers across the Mississippi Basin, and the extent of maize, soybean and wheat cultivation in the watersheds. Results The crop datasets provide a spatially explicit representation of the area of the three primary crops in 1950, 1970 and 1992. The datasets clearly depict the rapid expansion of soybean cultivation, the increased specialization of individual agricultural regions, and the accompanying reduction in agricultural biodiversity since 1950. The statistical analysis identified strong correlations between the extent of maize and soybean cover in a watershed and the level of nitrogen (N) and phosphorous (P) at the watershed outlet. In particular, the area of maize appears to be strongly related to the concentration of total‐N and the ratio of dissolved inorganic‐N and organic‐N at the watershed outlet. Conclusions The intensification of cultivation of the three primary crops — maize, soybean and wheat — has altered land cover and water quality across the U.S. since 1950. The high present‐day rate of fertilizer use on maize and the expansion of soybean cultivation could be largely responsible for the change in nutrient ratios in the Mississippi River since 1950.     

Bacterioplankton of the Gdansk Basin,Baltic Sea

The numbers, biomass, and production of bacterioplankton were determined in the Russian Sector of the Gdansk Basin (Baltic Sea) in 2007–2009. Significant spatial and temporal variations were determined. During the year, bacterial activity increased with increasing water temperature and higher availability of organic substrates. The lowest bacterial production (0.01–31.63 mg C m⁻³ day⁻¹) was observed in late winter and late autumn, while the highest (0.17–341.70 mg C m⁻³ day⁻¹) occurred in spring and summer. Since bacterial numbers and biomass were found to depend on the weather conditions and the terrigenous inflow, significant variations were observed from year to year. The highest and lowest numbers and biomass of bacterioplankton determined in summer were 0.09–1.10 × 10⁶ cells mL⁻¹ and 2–22 mg C m⁻³ for July 2007 and 1.96–11.23 × 10⁶ cells mL⁻¹ and 23–123 mg C m^–3 for July 2009. The values of these parameters were the highest along the coast and decreased towards the open sea.     

Migratory Patterns of Wild Chinook Salmon Oncorhynchus tshawytscha Returning to a Large,Free-Flowing River Basin

Upriver movements were determined for Chinook salmon Oncorhynchus tshawytscha returning to the Yukon River, a large, virtually pristine river basin. These returns have declined dramatically since the late 1990s, and information is needed to better manage the run and facilitate conservation efforts. A total of 2,860 fish were radio tagged during 2002–2004. Most (97.5%) of the fish tracked upriver to spawning areas displayed continual upriver movements and strong fidelity to the terminal tributaries entered. Movement rates were substantially slower for fish spawning in lower river tributaries (28–40 km d^-1) compared to upper basin stocks (52–62 km d^-1). Three distinct migratory patterns were observed, including a gradual decline, pronounced decline, and substantial increase in movement rate as the fish moved upriver. Stocks destined for the same region exhibited similar migratory patterns. Individual fish within a stock showed substantial variation, but tended to reflect the regional pattern. Differences between consistently faster and slower fish explained 74% of the within-stock variation, whereas relative shifts in sequential movement rates between “hares” (faster fish becoming slower) and “tortoises” (slow but steady fish) explained 22% of the variation. Pulses of fish moving upriver were not cohesive. Fish tagged over a 4-day period took 16 days to pass a site 872 km upriver. Movement rates were substantially faster and the percentage of atypical movements considerably less than reported in more southerly drainages, but may reflect the pristine conditions within the Yukon River, wild origins of the fish, and discrete run timing of the returns. Movement data can provide numerous insights into the status and management of salmon returns, particularly in large river drainages with widely scattered fisheries where management actions in the lower river potentially impact harvests and escapement farther upstream. However, the substantial variation exhibited among individual fish within a stock can complicate these efforts.     

A potential integrated water quality strategy for the Mississippi River Basin and the Gulf of Mexico

Nutrient pollution, now the leading cause of water quality impairment in the U.S., has had significant impact on the nation"s waterways. Excessive nutrient pollution has been linked to habitat loss, fish kills, blooms of toxic algae, and hypoxia (oxygen-depleted water). The hypoxic "dead zone" in the Gulf of Mexico is one of the most striking illustrations of what can happen when too many nutrients from inland watersheds reach coastal areas. Despite programs to improve municipal wastewater treatment facilities, more stringent industrial wastewater requirements, and agricultural programs designed to reduce sediment loads in waterways, water quality and nutrient pollution continues to be a problem, and in many cases has worsened. We undertook a policy analysis to assess how the agricultural community could better reduce its contribution to the dead zone and also to evaluate the synergistic impacts of these policies on other environmental concerns such as climate change. Using a sectorial model of U.S. agriculture, we compared policies including untargeted conservation subsidies, nutrient trading, Conservation Reserve Program extension, agricultural sales of carbon and greenhouse gas credits, and fertilizer reduction. This economic and environmental analysis is watershed-based, primarily focusing on nitrogen in the Mississippi River basin, which allowed us to assess the distribution of nitrogen reduction in streams, environmental co-benefits, and impact on agricultural cash flows within the Mississippi River basin from various options. The model incorporates a number of environmental factors, making it possible to get a more a complete picture of the costs and co-benefits of nutrient reduction. These elements also help to identify the policy options that minimize the costs to farmers and maximize benefits to society.     

Virio- and Bacterioplankton of the Coastal Water of the Moscow River

Doklady Biological Sciences - The first study on the dynamics of virioplankton abundance (VA) in the coastal waters of the Moscow River in the autumn–winter period at stations differing in...     

Diagnostic SNPs reveal widespread introgressive hybridization between introduced bighead and silver carp in the Mississippi River Basin

Hybridization among conspecifics in native and introduced habitats has important implications for biological invasions in new ecosystems. Bighead (Hypophthalmichthys nobilis) and silver carp (H. molitrix) are genetically isolated and occur in sympatry within their native range. Following their introduction to North America, however, introgressant hybrids have been reported throughout their expanded range within the Mississippi River Basin (MRB). The extent of introgression, both spatially and generationally, is largely unknown. Therefore, we examined mixed‐species populations from across the MRB to characterize the extent of interspecific gene flow. We assayed 2798 individuals from nine locations with a suite of species‐diagnostic SNPs (57 nuclear and one mitochondrial). Forty‐four per cent (n = 1244) of individuals displayed hybrid genotypes. Moreover, the composition of hybrid genotypes varied among locations and represented complex hybrid swarms with multiple generations of gene flow. Introgressive hybrids were identified from all locations, were bidirectional and followed a bimodal distribution consisting primarily of parental or parental‐like genotypes and phenotypes. All described hybrid categories were present among individuals from 1999 to 2008, with parents and later‐generation backcrosses representing the largest proportion of individuals among years. Our mitochondrial SNP (COII), tested on a subset of 730 individuals, revealed a silver carp maternal bias in 13 of 21 (62%) F₁ hybrids, in all silver carp backcrosses, and maintained throughout many of the bighead carp backcrosses. The application of this suite of diagnostic markers and the spatial coverage permits a deeper examination of the complexity in hybrid swarms between two invasive, introduced species.     

Shifting Biogeographic Patterns of Microcebus ravelobensis and M. murinus

International Journal of Primatology - It is important to understand how sympatric congeners can co-occur within the same landscapes to better understand niche differentiation and how each species...     

Common carp in the Upper Mississippi River

Since its escapement into the Upper Mississippi River (UMR) and rapid expansion in the late 1900's, the common carp, Cyprinus carpio, has become a major component of the river fishery. Mean annual harvest value for this species was $270000 between 1953 and 1977. Recent evidence suggests that common carp may not be as abundant in the river as they have been in the past. We summarized historical commerical information on common carp in the UMR to put its current harvest levels in perspective. A major factor responsible for recent low annual harvests has been PCB contamination of the river in the Lake Pepin area. Market and biological factors probably have also contributed to declining harvests. To help explain why common carp populations in the UMR may be declining, we reviewed literature pertaining to the ecology of the species, particularly that from the river, its tributaries, or midwestern lakes. We included information on how common carp are controlled by environmental factors, and how they interact with other biota. Most aspects of carp ecology in the UMR and other areas are similar. Exceptions relate primarily to their response to annual water level regimes of the river. We postulate that population declines and absent year classes in the UMR may be related to poor recruitment during high- or variable-water years.     

Concordant Biogeographic Patterns among Multiple Taxonomic Groups in the Mexican Freshwater Biota

In this paper we analyse the degree of concordance in species richness and taxonomic distinctness (diversity) patterns among different freshwater taxonomic groups in order to test three long held patterns described in Mexican freshwater biogeography: 1. The aquatic biota of Mexico includes two distinct faunas, a rich Neotropical component in the south and a south-eastern region and a less rich Nearctic component towards central and northern latitudes of the country. 2. A hotspot of species richness and diversity has been recorded in the Usumacinta, including the Yucatan Peninsula. 3. The presence of two distinct biotas in Mexico, an eastern one distributed along the Gulf of Mexico slope, and a western one associated to the Pacific versant. We use species richness and taxonomic distinctness to explore patterns of diversity and how these patterns change between zoogeographical regions. This paper points out a clear separation between Neotropical and Nearctic drainage basins but also between eastern (Gulf of Mexico) and western (Pacific) drainage basins. Present data gives additional empirical support from freshwater biota for three long held beliefs regarding distributional patterns of the Mexican biota. The neotropical basins of Mexico are generally host to a richest and more diversified fauna, that includes more families, genera and species, compared to the less rich and less diverse fauna in the nearctic basins.