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.     

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.     

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.     

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.     

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.     

Distribution Patterns of Indigenous Freshwater Fishes in the Tagus River Basin, Spain

Classification and ordination methods used to examine the internal complexity of the Mediterranean Tagus River catchment based on fish distribution revealed that it is not a homogeneous biogeographical unit. The indigenous fishes analyzed in this study are distributed through the basin forming geographical communities (chorotypes), some of which are associated with environmental factors like river morphology, water quality or geographical location. Nevertheless, 40% of the variation in species occurrence remains unexplained by either environmental or geographical variables, suggesting that historical factors may influence the freshwater fish distribution patterns. Three main biogeographical areas, delimited by significant boundaries, were identified. Two of them are identified as the upper and the middle-lower basins of the Tagus River catchment; the third corresponds to the Alagón River and seems to be linked to historical factors of the catchment.     

Temporal Patterns of Larval Fish Occurrence in a Large Subtropical River

Knowledge of temporal patterns of larval fish occurrence is limited in south China, despite its ecological importance. This research examines the annual and seasonal patterns of fish larval presence in the large subtropical Pearl River. Data is based on samples collected every two days, from 2006 to 2013. In total, 45 taxa representing 13 families and eight orders were sampled. The dominant larval family was Cyprinidae, accounting for 27 taxa. Squaliobarbus curriculus was the most abundant species, followed by Megalobrama terminalis, Xenocypris davidi, Cirrhinus molitorella, Hemiculter leuscisculus and Squalidus argentatus. Fish larvae abundances varied significantly throughout the seasons (multivariate analyses: Cluster, SIMPROF and ANOSIM). The greatest numbers occurred between May and September, peaking from June through August, which corresponds to the reproductive season. In this study, redundancy analysis was used to describe the relationship between fish larval abundance and associated environmental factors. Mean water temperature, river discharge, atmospheric pressure, maximum temperature and precipitation play important roles in larval occurrence patterns. According to seasonal variations, fish larvae occurrence is mainly affected by water temperature. It was also noted that the occurrence of Salanx reevesii and Cyprinus carpio larvae is associated with higher dissolved oxygen (DO) concentrations, higher atmospheric pressure and lower water temperatures which occur in the spring. On the other hand, M. terminalis, X. davidi, and C. molitorella are associated with high precipitation, high river discharge, low atmospheric pressure and low DO concentrations which featured during the summer months. S. curriculus also peaks in the summer and is associated with peak water temperatures and minimum NH₃–N concentrations. Rhinogobius giurinus occur when higher atmospheric pressure, lower precipitation and lower river discharges occur in the autumn. Dominant fish species stagger their spawning period to avoid intraspecific competition for food resources during early life stages; a coexistence strategy to some extent. This research outlines the environmental requirements for successful spawning for different fish species. Understanding processes such as those outlined in this research paper is the basis of conservation of fish community diversity which is a critical resource to a successful sustainable fishery in the Pearl River.     

Constructed Crevasses and Land Gain in the Mississippi River Delta

Extensive land loss, which is mostly wetland loss, has taken place during this century in the Mississippi River delta and other river deltas. Our purpose was to evaluate the effectiveness of constructing “artificial” crevasses, or cuts in the natural levee, made by the U.S. Fish and Wildlife Service in the Delta National Wildlife Refuge (DNWR) to slow or reverse this type of land loss. Land growth of the crevasses was determined from aerial photographs and was related to crevasse-site characteristics. The newly constructed crevasses create emergent wetlands after 2 years of subaqueous growth at about 4.7 ha/year and an average cost of $21,377 per crevasse. The present total cost per hectare declines with age as new land builds, and it will equal $48 per hectare if all the open water in the receiving ponds fills in. At these rates, the net land loss rates in the DNWR measured from 1958 to 1978 would be compensated for by the building of 63 crevasses, 24 of which are already in place.     

Seasonal succession of the phytoplankton in the upper Mississippi River

Species composition and seasonal succession of the phytoplankton were investigated on the upper Mississippi River at Prairie Island, Minnesota, U.S.A. Both the numbers and volume of individual species were enumerated based on cell counts with an inverted microscope. A succession similar to algal succession in the local lakes occurred. The diatoms were dominant during the spring and fall and blue-green algae were dominant during the summer. The algal concentrations have increased up to 40 fold the concentrations of the 1920's, since the installation of locks and dams. The maximum freshweight standing crop was 4 mg · l^–1 in 1928 (Reinhard 1931), 13 mg · l^–1 in 1975 a wet year, and 47 mg · l^–1 in 1976, a relatively dry year with minimal current discharge. The diatoms varied from 36–99%, the blue-green algae from 0–44% and the cryptómonads from 0–50% of the total standing crop. The green algae were always present but never above 21% of the biomass. The dominant diatoms in recent years were centric -Stephanodiscus andCyclotella spp. (maximum 50,000 ml^–1). The dominant blue-green algae wereAphanizomenon flos-aquae (L.) Ralfsex Born.et Flahault andOscillatoria agardhii Gomont (maximum 800 ml^–1). These algal species are also present in local lakes. Shannon diversity values indicated greatest diversity of algae during the summer months.     

Age and growth of pallid sturgeon in the free-flowing Mississippi River

Trotlines were used to capture pallid sturgeon in the free‐flowing Mississippi River, which extends from the Gulf of Mexico to the mouth of the Missouri River. Trotlines were baited with worms, and set overnight usually along the channel border. The pectoral fin rays of 165 pallid sturgeon caught in the Mississippi River were aged; 118 were from the lower Mississippi River (LMR) between the Gulf and mouth of the Ohio River, and 47 were from the middle Mississippi River (MMR) between the mouths of the Ohio and Missouri rivers. Initial agreement within ±1 year between two readers ranged from 53% for the LMR specimens, which were read first, to 84% for the MMR. Final age was agreed upon by both readers. For LMR pallid sturgeon, final age estimates ranged from 3 to 21 years with a mean (±SD) of 11.0 ± 4.7. For MMR pallid sturgeon, final age estimates ranged from 5 to 14 years with a mean of 9.5 ± 2.1. Seven pallid sturgeon marked with coded wire tags (CWT), indicating hatchery origin, were collected in the MMR. Age estimates for CWT fish were 7–8 years representing 1997 stocked fish, and 11–12 years representing 1992 progeny stocked in 1994. Von Bertalanffy growth equations for length indicated that pallid sturgeon in the MMR had higher growth rates for a given age than pallid sturgeon in the LMR. However, there were no significant differences (anova , P > 0.5) in the length–weight relationships between reaches. In the LMR, pallid sturgeon fully recruited to trotlines at age 11 and instantaneous total mortality (Z; slope of catch curve) was estimated at −0.12 (n = 10 year classes, r² = 0.55, P = 0.01). Of the 118 sectioned rays from the LMR, 28 could not be reliably aged (only one section from the MMR could not be aged). Therefore, age was predicted from length using the von Bertalanffy equation. The catch curve was re‐calculated using the predicted ages of the 28 pallid sturgeon in the LMR resulting in Z = −0.07. In the MMR, pallid sturgeon fully recruited to trotlines at age 9 and Z was estimated at −0.36 (n = 6 year classes, r² = 0.67, P = 0.04), which was significantly higher (anova , P = 0.04) than the LMR estimate. Higher mortality in the MMR may be due to habitat limitations compared to a larger, more diverse channel in the LMR, and incidental take of larger, older individuals during commercial harvesting of shovelnose sturgeon. Commercial take of shovelnose does not occur in the LMR except in the northern portion of the reach. Considering the presence of pallid sturgeon with CWT, recruitment of older individuals in the MMR may have been influenced by stocking a decade earlier. Management strategies for this endangered species should consider the differences in mortality rates among reaches, the impacts of commercial fishing on recovery of pallid sturgeon in the MMR, and the long‐term effects of hatchery fish now recruiting into the free‐flowing Mississippi River.     

Biogeographic Distribution Patterns and Their Correlates in the Diverse Frog Fauna of the Atlantic Forest Hotspot

Anurans are a highly diverse group in the Atlantic Forest hotspot (AF), yet distribution patterns and species richness gradients are not randomly distributed throughout the biome. Thus, we explore how anuran species are distributed in this complex and biodiverse hotspot, and hypothesize that this group can be distinguished by different cohesive regions. We used range maps of 497 species to obtain a presence/absence data grid, resolved to 50×50 km grain size, which was submitted to k-means clustering with v-fold cross-validation to determine the biogeographic regions. We also explored the extent to which current environmental variables, topography, and floristic structure of the AF are expected to identify the cluster patterns recognized by the k-means clustering. The biogeographic patterns found for amphibians are broadly congruent with ecoregions identified in the AF, but their edges, and sometimes the whole extent of some clusters, present much less resolved pattern compared to previous classification. We also identified that climate, topography, and vegetation structure of the AF explained a high percentage of variance of the cluster patterns identified, but the magnitude of the regression coefficients shifted regarding their importance in explaining the variance for each cluster. Specifically, we propose that the anuran fauna of the AF can be split into four biogeographic regions: a) less diverse and widely-ranged species that predominantly occur in the inland semideciduous forests; b) northern small-ranged species that presumably evolved within the Pleistocene forest refugia; c) highly diverse and small-ranged species from the southeastern Brazilian mountain chain and its adjacent semideciduous forest; and d) southern species from the Araucaria forest. Finally, the high congruence among the cluster patterns and previous eco-regions identified for the AF suggests that preserving the underlying habitat structure helps to preserve the historical and ecological signals that underlie the geographic distribution of AF anurans.