Structuring of bacterioplankton communities by specific dissolved organic carbon compounds

The main role of microorganisms in the cycling of the bulk dissolved organic carbon pool in the ocean is well established. Nevertheless, it remains unclear if particular bacteria preferentially utilize specific carbon compounds and whether such compounds have the potential to shape bacterial community composition. Enrichment experiments in the Mediterranean Sea, Baltic Sea and the North Sea (Skagerrak) showed that different low-molecular-weight organic compounds, with a proven importance for the growth of marine bacteria (e.g. amino acids, glucose, dimethylsulphoniopropionate, acetate or pyruvate), in most cases differentially stimulated bacterial growth. Denaturing gradient gel electrophoresis 'fingerprints' and 16S rRNA gene sequencing revealed that some bacterial phylotypes that became abundant were highly specific to enrichment with specific carbon compounds (e.g. Acinetobacter sp. B1-A3 with acetate or Psychromonas sp. B3-U1 with glucose). In contrast, other phylotypes increased in relative abundance in response to enrichment with several, or all, of the investigated carbon compounds (e.g. Neptuniibacter sp. M2-A4 with acetate, pyruvate and dimethylsulphoniopropionate, and Thalassobacter sp. M3-A3 with pyruvate and amino acids). Furthermore, different carbon compounds triggered the development of unique combinations of dominant phylotypes in several of the experiments. These results suggest that bacteria differ substantially in their abilities to utilize specific carbon compounds, with some bacteria being specialists and others having a more generalist strategy. Thus, changes in the supply or composition of the dissolved organic carbon pool can act as selective forces structuring bacterioplankton communities.     

Distribution of loliginid squids in a eutrophicated tropical coastal bay

Guanabara Bay is one of the most polluted bays in Brazil, although it supports some fisheries resources, among which are three species of loliginid squids: Lolliguncula brevis, Doryteuthis plei, and Doryteuthis sanpaulensis. This study aimed to assess the temporal and spatial variations of squids in the bay, relating their abundance variation to local environmental factors. We also aimed to characterize the population structure of squids, in order to establish their degree of occupancy in this estuarine system. Ten fortnightly hauls were carried out (two per area) from July 2005 to June 2007. Squids were identified, measured, weighed, sexed and classified according to maturity stage. The spatial distribution of the three species was not uniform; most individuals were found near the mouth of the bay. Abundances were significantly different among seasons due to the presence of SACW (South Atlantic Central Water) during the spring–summer season. Most of the populations of the three species consist of juveniles, and most adult Doryteuthis were also immature, which reinforces the role of Guanabara Bay as a nursery ground for loliginid squids. Concerning the degree of occupancy of squids in Guanabara Bay, L. brevis is considered an estuarine resident, D. plei uses the estuarine system as a nursery area for feeding and growth, and juveniles of D. sanpaulensis enter the bay with the flood tide to feed, generally following the SACW intrusion. This is the first study on squids in this estuarine system, which despite the high degree of environmental impact is shown to be an important area for the loliginid species.     

Flow cytometry assessment of bacterioplankton in tropical marine environments

Flow cytometry was used to characterize bacterioplankton from two tropical environments in Brazil: the eutrophic Guanabara Bay and the oligotrophic southwest Atlantic Ocean. Bacterial abundance was evaluated by flow cytometry, and cells were stained with SYTO 13, allowing demonstration of differences in nucleic acid content. Bacterial production was also evaluated by means of 3H-leucine incorporation. Bacterial numbers were different for both sites. In Atlantic Ocean samples, we found a maximum of 5.50 x 10(5) cells ml(-1), and low nucleic acid content organisms predominated. In Guanabara Bay, bacterial numbers were one order of magnitude higher than in the ocean, and they varied from outer bay (1.01 x 10(6) cells ml(-1)) to inner bay (6.90 x 10(6) cells ml(-1)). Bacterial activity in ocean samples varied from 4.6 to 126 ng C l(-1) h(-1), while in the bay, mean values ranged from 1.95 microg C l(-1) h(-1) (outer bay) to 7.35 microg C l(-1) h(-1) (inner bay). Values found for both parameters are characteristic of different trophic situations. These results illustrate the utility of cytometric analyses of bacterioplankton populations in characterizing their large spatial and temporal scales of distribution in aquatic ecosystems.     

Spatial variations in macrobenthic fauna recolonisation in a tropical mangrove bay

Recolonisation by crab species and sediment-infauna taxa (at class level) in artificially regenerated mangrove stands of Avicennia marina, Rhizophora mucronata and Sonneratia alba (5 yr old) were studied using respective bare sites (open without mangroves or denuded) and natural sites (relatively undisturbed) as controls. The controls were chosen based on site history, physical proximity and tidal inundation class in reference to the particular reforested mangrove stand and samples randomly taken. A number of environmental variables were measured; interstitial water salinity and temperature (measured at low tide) were lower, whereas sediment organic matter content was higher in the areas with mangrove cover, with the natural sites having the highest content. The bare sites were generally sandier, whereas the areas with mangrove cover had higher proportions of clay and silt. Generally, there was a higher crab density in the reforested sites than in the bare sites, whereas crab species diversity (Shannon diversity index) did not vary from one site to another for any of the mangrove species. In terms of crab species composition, the reforested sites were more similar (Sørensen similarity coefficient) to the natural sites and less to the bare controls. For sediment-infauna, the reforested sites had a significantly higher density than the respective bare controls, while the natural sites had the highest density. The number of sediment-infauna taxa in both the reforested and natural sites of all the mangrove species was similar and higher than in the comparable bare sites. The results suggest that the reforested sites are supporting more faunal recolonisation, and therefore becoming more akin to the natural mangrove sites in terms of the investigated functional indicators. The findings seem to support the use of artificial mangrove regeneration (in areas where natural regeneration has been impeded by physical conditions or otherwise) as an effective management tool in the restoration and conservation of the functional integrity of degraded mangrove habitats.Key words: Crabs, Environmental variables, Kenya, Recolonisation, Restored mangroves, Sediment-infauna     

Protozooplankton and bacterioplankton in a large oligotrophic lake--Loch Ness, Scotland

The seasonal changes in the abundance of protozoan and bacterialplankton in a large, coloured, oligotrophic lake. Loch Ness(Scotland), were investigated between August 1991 and January1993. The coloured water supported only low concentrations ofchlorophyll a (<1.6 µgl^–1). with the highestvalues occurring in summer. Mean bacterial abundance rangedbetween 2.3 x 10⁸ and 7.1 x 10⁸ l^–1 in the 100 m watercolumn. Maximum abundance did not correlate with maximum chlorophylla concentrations, but appeared to be related to the input ofallochthonous carbon from the catchment, which in turn was influencedby rainfall levels. Consequently, the highest bacterioplanktonconcentrations occurred in autumn and winter. The pattern ofheterotrophic nanoflagellate abundance tended to follow thatfor bacteria, with mean concentrations in the top 100 m of thewater column of between 12 x 10³ and 273 x 10³ l^–1. Ciliateabundance showed no seasonal trends over the study period andprobably mirrored the fluctuating availability of various foodresources. Oligotrichs, particularly mixotrophic taxa, werea prominent element of the community throughout the year. Aggregatesof detrital material were a regular feature in the plankton.When these occurred, they formed foci for bacteria and nanoflagellates.The evidence suggests that the dynamics of the microbial planktonin Loch Ness may be driven by allochthonous carbon inputs ratherthan by the more usual dominance of carbon fixed within thesystem. ¹Present address: School of Zoology, La Trobe University, Bundoora,Melbourne, Victoria 3083, Australia ²Present address: Loch Ness & Morar Project, Loch Ness Centre,Drumnadrochit, Invernesshire, UK     

Loss of phytoplankton functional and taxonomic diversity induced by river regulation in a large tropical river

Hydrobiologia - Human activities have disrupted the functioning of river ecosystems around the world. In the Amazon basin, hydropower expansion has affected diversity patterns, but no study has...     

Low intraspecific diversity in a polynucleobacter subcluster population numerically dominating bacterioplankton of a freshwater pond

Cultivation-dependent and -independent methods were combined to investigate the microdiversity of a Polynucleobacter subcluster population (Betaproteobacteria) numerically dominating the bacterioplankton of a small, humic freshwater pond. Complete coverage of the population by cultivation allowed the analysis of microdiversity beyond the phylogenetic resolution of ribosomal markers. Fluorescent in situ hybridization with two probes specific for the narrow subcluster C (PnecC bacteria) of the Polynucleobacter cluster revealed that this population contributed up to 60% to the total number of bacterioplankton cells. Microdiversity was investigated for a date at which the highest relative numbers of PnecC were observed. A clone library of fragments of the ribosomal operon (16S rRNA genes, complete 16S-23S internal transcribed spacer 1 [ITS1], partial 23S rRNA genes) amplified with universal bacterial primers was constructed. The library was stepwise screened for fragments from PnecC bacteria and for different ITS genotypes of PnecC bacteria. The isolated PnecC strains were characterized by sequencing of the 16S rRNA genes and the ITS1. Both the clone library and the established culture collection contained only the same three ITS genotypes, and one of them contributed 46% to the entire number of clones. Genomic fingerprinting of the isolates with several methods always resulted in the detection of only one fingerprint per ITS genotype. We conclude that a Polynucleobacter population with an extremely low intraspecific diversity and an uneven structure numerically dominated the bacterioplankton community in the investigated habitat. This low intraspecific diversity is in strong contrast to the high intraspecific diversities found in marine bacterial populations.     

Functional diversity and trait–environment relationships of stream fish assemblages in a large tropical catchment

1. The species composition of stream fish assemblages changes across the longitudinal fluvial gradient of large river basins. These changes may reflect both zonation in species distributions and environmental filtering of fish traits as stream environments change from the uplands to the lowlands of large catchments. Previous research has shown that taxonomic diversity generally increases in larger, lowland streams, and the River Continuum Concept, the River Habitat Template and other frameworks have provided expectations for what functional groups of fishes should predominate in certain stream types. However, studies addressing the functional trait composition of fish assemblages across large regions are lacking, particularly in tropical river basins. 2. We examined functional trait–environment relationships and functional diversity of stream fish assemblages in the Río Grijalva Basin in southern Mexico. Traits linked to feeding, locomotion and life history strategy were measured in fishes from streams throughout the catchment, from highland headwaters to broad, lowland streams. Relationships between functional traits and environmental variables at local and landscape scales were examined using multivariate ordination, and the convex hull volume of trait space occupied by fish assemblages was calculated as a measure of functional diversity. 3. Although there were a few exceptions, functional diversity of assemblages increased with species richness along the gradient from uplands to lowlands within the Grijalva Basin. Traits related to swimming, habitat preference and food resource use were associated with both local (e.g. substratum type, pool availability) and landscape‐scale (e.g. forest cover) environmental variables. 4. Along with taxonomic structure and diversity, the functional composition of fish assemblages changed across the longitudinal fluvial gradient of the basin. Trait–environment relationships documented in this study partially confirmed theoretical expectations and revealed patterns that may help in developing a better understanding of general functional responses of fish assemblages to environmental change.     

The dynamics of heterotrophic nanoflagellates and bacterioplankton in a large ultra-oligotrophic Antarctic lake

The abundance of both heterotrophic nanoflagellates (HNAN) andbacterioplankton in a large (9km²) ultraoligotrophic Antarcticlake (Crooked Lake) were investigated from December 1992 untilNovember 1993. HNAN abundance peaked in spring, summer and autumn,falling to lowest numbers during the winter. Numbers rangedbetween 0 and 50.9x10⁴ l^–1. Bacterioplankton abundancewas highest during the late summer and then fell progressivelytowards winter and autumn (range 1.19–4.46x10⁶ l^–1)In contrast to numbers, mean cell volumes (MCV) of the bacteriareached their highest in spring, and consequently highest bacterialbiomass occurred at this time. MCV ranged between 0.052 and0.224µm³. Bacterial production measurements followingthe incorporation of [³H] thymidine into DNA and [¹⁴C] leucineinto protein using a doubling-labelling procedure were undertakenin January, June, August, October and November. Rates variedbetween 2.8 and 52 ng C l¹ h¹. On occasions, a significant differencein production rates based on the uptake of leucine and thymidinewas observed, suggesting unbalanced growth. Highest rates ofproduction coincided with times of high dissolved organic carbonlevels in the water column and lowest production with low levelsof DOC. HNAN grazing rates were measured by following the uptakeof fluorescently labelled bacteria and averaged 4.8 bacterialcells individual¹ day¹ at 2 and 4°C. Specific growth rates(h¹) ranged around 0.00070–0.00077 in both the field andlaboratory, giving doubling times of 37.3 and 41.0 days, respectively.These low rates of grazing and growth indicate that there isno adaptation to low temperatures in these freshwater protists.Based on these data, the gross production efficiency is 24%.HNAN removed between 0.1 and 9.7% of bacterial production perday.     

Global patterns of diversity and community structure in marine bacterioplankton

Because of their small size, great abundance and easy dispersal, it is often assumed that marine planktonic microorganisms have a ubiquitous distribution that prevents any structured assembly into local communities. To challenge this view, marine bacterioplankton communities from coastal waters at nine locations distributed world-wide were examined through the use of comprehensive clone libraries of 16S ribosomal RNA genes, used as operational taxonomic units (OTU). Our survey and analyses show that there were marked differences in the composition and richness of OTUs between locations. Remarkably, the global marine bacterioplankton community showed a high degree of endemism, and conversely included few cosmopolitan OTUs. Our data were consistent with a latitudinal gradient of OTU richness. We observed a positive relationship between the relative OTU abundances and their range of occupation, i.e. cosmopolitans had the largest population sizes. Although OTU richness differed among locations, the distributions of the major taxonomic groups represented in the communities were analogous, and all local communities were similarly structured and dominated by a few OTUs showing variable taxonomic affiliations. The observed patterns of OTU richness indicate that similar evolutionary and ecological processes structured the communities. We conclude that marine bacterioplankton share many of the biogeographical and macroecological features of macroscopic organisms. The general processes behind those patterns are likely to be comparable across taxa and major global biomes.     

Diapause in a large aggregation of a tropical beetle

Abstract. 1_˜ Diapause is described for adults of Stenotarsus rotundus Arrow (Endomychidae, Coleoptera) in the tropical lowland forest on Barro Colorado Island, Panama.
2 . Diapause lasted up to 10 months each year, covering some 6 months of the wet season plus 4 months of the dry season. When in diapause the beetles clustered in an aggregation of up to 70 ,000 individuals on the stem of a palm tree, the same individual palm tree in at least four successive years.
3. The habitat and habits of the beetle when not in diapause are unknown, but one or two generations may be produced during this period. Beetles returned to the diapause site from June until late August.
4. Soon after arrival at the diapause site the flight muscles degenerated and did not develop again until February/March. The ovaries were undeveloped when the beetles arrived at the site and remained in that condition until the onset of yolk deposition in March. At the beginning of the rainy season in April the beetles mated and dispersed.
5. Lean dry weight of the beetles did not decrease noticeably during diapause, but fat content did. It is suggested that the beetles do not feed, or feed very little, while in diapause. During diapause, the metabolic rate is surprisingly low considering a mean ambient temperature of 25° C.
6. Juvenile hormone analogue (ZR515) stimulated flight muscle and ovary development. Daylength, when different from LD 12: 12 , initiated a partial flight muscle development, but there was no effect on the ovaries. Field observations suggest that neither temperature nor humidity had an effect on the termination of diapause.
7. Although the development of both flight muscles and ovaries were stimulated by juvenile hormone analogue and both developed around March of each year, it is suggested that the mechanisms causing this development are different.     

Temporal variability in the diversity and composition of stream bacterioplankton communities

Bacterioplankton in freshwater streams play a critical role in stream nutrient cycling. Despite their ecological importance, the temporal variability in the structure of stream bacterioplankton communities remains understudied. We investigated the composition and temporal variability of stream bacterial communities and the influence of physicochemical parameters on these communities. We used barcoded pyrosequencing to survey bacterial communities in 107 streamwater samples collected from four locations in the Colorado Rocky Mountains from September 2008 to November 2009. The four sampled locations harboured distinct communities yet, at each sampling location, there was pronounced temporal variability in both community composition and alpha diversity levels. These temporal shifts in bacterioplankton community structure were not seasonal; rather, their diversity and composition appeared to be driven by intermittent changes in various streamwater biogeochemical conditions. Bacterial communities varied independently of time, as indicated by the observation that communities in samples collected close together in time were no more similar than those collected months apart. The temporal turnover in community composition was higher than observed in most previously studied microbial, plant or animal communities, highlighting the importance of stochastic processes and disturbance events in structuring these communities over time. Detailed temporal sampling is important if the objective is to monitor microbial community dynamics in pulsed ecosystems like streams.     

Diversity of bacterial communities related to the nitrogen cycle in a coastal tropical bay

A culture-independent molecular phylogenetic analysis was carried out to study for the first time the diversity of bacterial ammonia monooxygenase subunit A (amoA) and nitrogenase reductase subunit H (nifH) genes from Urca inlet at Guanabara Bay in Rio de Janeiro, Brazil. Most bacterial amoA and nifH sequences exhibited identities of less than 95% to those in the GenBank database revealing that novel ammonia-oxidizing bacteria and nitrogen-fixing microorganisms may exist in this tropical marine environment. The observation of a large number of clones related to uncultured bacteria also indicates the necessity to describe these microorganisms and to develop new cultivation methodologies.     

Phenological diversity in tropical forests

One of the most intriguing and complex characteristics of reproductive phenology in tropical forests is high diversity within and among forests. To understand such diversity, Newstrom et al. provided a systematic framework for the classification of tropical flowering phenology. They adopted frequency and regularity as criteria with priority, and classified plants in La Selva, Costa Rica, where most plants reproduced more than once a year irregularly. Many other studies have demonstrated annual cycles corresponding to rainfall patterns at the community level in Neotropical forests, including La Selva. On the other hand, supraannual flowering synchronized among various plant species, called general flowering, is known from aseasonal lowland dipterocarp forests in Southeast Asia. Within both forests, a wide spectrum of flowering patterns is found. This range of patterns suggests the great potential of tropical phenological studies to explore the selective pressures on phenology. Various abiotic and biotic factors can be selective agents. The shared pollinators hypothesis suggests that plant species sharing pollinators segregate flowering temporarily to minimize interspecific overlap in flowering times and thus minimize ineffective pollination or competition for pollinators, indicating strong phylogenetic constraints in timing and variation of flowering. Comparison of phenology within and among forests may help our understanding of phenological diversity. Attempts are now being made to develop a common language to communicate concepts and render interpretations of data more compatible among investigators and to create a network to promote comparative studies. Received: September 8, 2000 / Accepted: January 30, 2001     

Species diversity and dominance in a tropical grassland community

Plant species diversity and dominance patterns were studied in a tropical grassland comunity at Berhampur, India during 1977–1978. Diversity (?Σpilnpi) and dominance [Σ(ni/N) ²] indices were calculated and compared with basic data as the number of individuals versus basic data as biomass units.     

Nitrogen fixing bacterial diversity in a tropical estuarine sediments

Microorganisms play a significant role in biogeochemical cycles, especially in the benthic and pelagic ecosystems. Role of environmental parameters in regulating the diversity, distribution and physiology of these microorganisms in tropical marine environment is not well understood. In this study, we have identified dinitrogen (N₂) fixing bacterial communities in the sediments by constructing clone libraries of nitrogenase (nifH) gene from four different stations in the Cochin estuary, along the southeastern Arabian Sea. N₂ fixing bacterial clones revealed that over 20 putative diazotrophs belong to alpha-, beta-, gamma-, delta- and epsilon- proteobacteria and firmicutes. Predominant genera among these were Bradyrhizobium sp. (α-proteobacteria), Dechloromonas sp. (β-proteobacteria); Azotobactor sp., Teredinibacter sp., Methylobacter sp., Rheinheimera sp. and Marinobacterium sp. (γ-proteobacteria); Desulfobacter sp., Desulfobulbus sp. and Desulfovibrio sp. (δ -proteobacteria); Arcobacter sp. and Sulfurospirillum sp. (ε-proteobacteria). Nostoc sp. was solely identified among the cyanobacterial phylotype. Nitrogen fixing Sulfate reducing bacteria (SRBs) such as Desulfobulbus sp., Desulfovibrio sp., Desulfuromonas sp., Desulfosporosinus sp., Desulfobacter sp., were also observed in the study. Most of the bacterial nifH sequences revealed that the identities of N₂ fixing bacteria were less than 95% similar to that available in the GenBank database, which suggested that the sequences were of novel N₂ fixing microorganisms. Shannon-Weiner diversity index of nifH gene ranged from 2.95 to 3.61, indicating an inflated diversity of N₂ fixing bacteria. Canonical correspondence analysis (CCA) implied positive correlation among nifH diversity, N₂ fixation rate and other environmental variables.     

Beta diversity of orchid bees in a tropical biodiversity hotspot

A controversial issue in ecology and conservation is whether community composition is controlled by niche or dispersal assembly. We assessed the importance of climatic factors and geographic gradients on the distribution of orchid bees in a severely-fragmented and species-rich tropical forest region in Brazil. Orchid-bee males were attracted to 17 different scent baits and collected in 15 forest sites. In total we captured 11,081 bees from 40 species. Climatic variables explained twice as much of the observed variation in the bee species data set as did pure spatial variation. However, most of the climatic explained variation was spatially structured, indicating that the species and the climatic data have a similar spatial arrangement. In fact, part of the observed latitudinal changes in community composition appears to be explained by a concomitant gradient in precipitation seasonality. Similarly, reduced temperatures and a more seasonal precipitation may help to explain the relative distinctiveness of the fauna from some of the westernmost sites. The level of similarity among the sampled sites, although highly variable, decayed both as function of the climatic and geographic distances among these sites. The greatest pairwise dissimilarities in the composition of the orchid-bee fauna were observed among sites 200–300 km from each other, since in many case those sites were more dissimilar in terms of climate than those further apart. It is suggested that global warming and consequent altered climatic regimes will influence the distribution patterns of orchid bees in a region already threatened by deforestation and forest fragmentation.