Seasonal dynamics of ammonia-oxidizing microorganisms in freshwater aquaculture ponds

An annual investigation into the abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in fresh water aquaculture ponds was performed by quantitative PCR of the amoA gene. The results showed that AOB were the main ammonia-oxidizing microorganisms in water, and significantly higher copy numbers of the AOB amoA gene were observed in the summer (Aug 2012), while no significant differences were detected among the other three seasons. AOA showed low abundances throughout the year. The predominance of AOB in aquaculture water was suggested to be related to photoinhibition. Both the AOB and AOA amoA genes in aquaculture pond sediments showed typical seasonal patterns. The maximum density of AOB was observed in the autumn (Nov 2012) and winter (Jan 2013), while the maximum density of AOA was observed in winter. The minimum densities of both AOA and AOB occurred in the summer. The concentration of the AOA amoA gene was higher than that of the AOB amoA gene in sediments by almost one order of magnitude, which indicates that AOA are the dominant ammonia-oxidizing microorganisms in the aquaculture pond sediments. Dissolved oxygen is suggested to be the key factor determining the predominance of AOA in pond sediments.     

Distribution of sediment bacterial and archaeal communities in plateau freshwater lakes

Both Bacteria and Archaea might be involved in various biogeochemical processes in lacustrine sediment ecosystems. However, the factors governing the intra-lake distribution of sediment bacterial and archaeal communities in various freshwater lakes remain unclear. The present study investigated the sediment bacterial and archaeal communities in 13 freshwater lakes on the Yunnan Plateau. Quantitative PCR assay showed a large variation in bacterial and archaeal abundances. Illumina MiSeq sequencing illustrated high bacterial and archaeal diversities. Bacterial abundance was regulated by sediment total organic carbon and total nitrogen, and water depth, while nitrate nitrogen was an important determinant of bacterial diversity. Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, and Verrucomicrobia were the major components of sediment bacterial communities. Proteobacteria was the largest phylum, but its major classes and their proportions varied greatly among different lakes, affected by sediment nitrate nitrogen. In addition, both Euryarchaeota and Crenarchaeota were important members in sediment archaeal communities, while unclassified Archaea usually showed the dominance.     

Implications of species loss in freshwater fish assemblages

Freshwater systems are vulnerable to pollution and species loss often ensues. Are there additional implications for assemblage structure? Here we use Berger‐Parker d. Simpson's I/D and Simpson's F to measure the ecological diversity of pristine and perturbed freshwater fish assemblages in Trinidad. West Indies, and Oklahoma. USA. Although the impacted sites typically had fewer species than expected, they could not be distinguished from unperturbed ones of equivalent richness. Changes in the evenness of these assemblages are thus driven by changes in richness. One practical outcome is that diversity indices may not provide independent verification of the detrimental consequences of pollution. The similarity in structure of naturally and anthropogenically impoverished assemblages provides no grounds for complacency, however, since it ignores the evolutionary history of the species concerned. On the basis of our results we suggest that species provenance may be important in tests of ecological function. Moreover, these investigations should replicate natural patterns of evenness as well as richness.     

Anaerobic methane oxidation potential and bacteria in freshwater lakes: Seasonal changes and the influence of trophic status

Nitrite-dependent anaerobic methane oxidation (n-damo), mainly carried out by n-damo bacteria, is an important pathway for mitigating methane emission from freshwater lakes. Although n-damo bacteria have been detected in a variety of freshwater lakes, their potential and distribution, and associated environmental factors, remain unclear. Therefore, the current study investigated the potential and distribution of anaerobic methanotrophs in sediments from Erhai Lake and Dianchi Lake, two adjacent freshwater lakes in the Yunnan Plateau with different trophic status. Both lakes showed active anaerobic methane oxidation potential and harbored a high density of n-damo bacteria. Based on the n-damo pmoA gene, sediment n-damo bacterial communities mainly consisted of Candidatus Methylomirabils oxyfera and Candidatus Methylomirabils sinica, as well as novel n-damo organisms. Sediment anaerobic methane oxidation potential and the n-damo bacterial community showed notable differences among seasons and between lakes. The environmental variables associated with lake trophic status (e.g. total nitrogen, ammonia nitrogen, nitrate nitrogen, and total organic carbon) might have significant impacts on the anaerobic methane oxidation potential, as well as the abundance and community structure of n-damo bacteria. Therefore, trophic status could determine the n-damo process in freshwater lake sediment.     

Seasonal changes in the character and nitrogen content of dissolved organic matter in an alpine/subalpine headwater catchment

We are studying the chemical quality of dissolved organic nitrogen (DON) in a high-elevation watershed in the Colorado Front Range. Samples were collected over the 2000 snowmelt runoff season at two sites across an alpine/subalpine ecotone to understand how the transition between the lightly vegetated alpine and forested reaches of the catchment influences the chemical character of DON. Samples were analyzed approximately weekly for dissolved organic material (DOM) content and chemical character. A subset of samples was analyzed for the elemental content of fulvic and hydrophilic acids. Concentrations of DON at both sites were highest in the spring at the initiation of snowmelt, decreased during snowmelt, and increased again during the late summer and fall. In contrast, concentrations of dissolved organic carbon (DOC) peaked on the ascending limb of the hydrograph and declined to seasonal minima on the descending limb of the hydrograph. The ratio of DOC:DON showed a seasonal shift at both sites with high values (40 to 55) during peak runoff in early summer and lower values (15 to 25) during low flows late in the runoff season. These results indicate that there was a seasonal change in the relative N content of DOM at both sites. Chemical fractionation of DOC showed that there were temporal and longitudinal changes in the chemical character of DOC. At the alpine site, the fulvic acid content of DOC decreased from 57% in June to 35% in September. The change in fulvic acid was less pronounced at the forested site, from 66% in June to 54% in September. Elemental analysis of fulvic and hydrophilic acids indicated that hydrophilic acids were N rich compared to fulvic acids. Additionally, fulvic and hydrophilic acids isolated at the alpine site had a lower C:N ratio than those isolated at the forested site. Similarly, the C:N ratio of organic acids at both sites was lower in September than in June during peak runoff. These differences appear to be a result of changes in both DOM precursor material and hydrologic flowpaths. Using C:N ratios of fulvic and hydrophilic acids, we estimate that nonhumic material carried between 54 to 73% of the organic N in surface water at the alpine site and 44 to 58% of the organic N in surface water at the subalpine site.     

Seasonal and spatial variance of seed bank species composition in an oligotrophic wet meadow

Seasonal and small-scale spatial variation of the seed bank in an oligotrophic wet meadow (Molinion) was assessed by two methods: (1) direct determination of seeds extracted from soil samples (6 cm in diameter, 10 cm depth) and (2) germination of seeds according to Ter Heerdt et al. [1996. An improved method for seed bank analysis: seedling emergence after removing the soil by sieving. Funct. Ecol. 10, 144–151]. Samples were taken three times during the year (July and November 2001, March 2002) from three distinct microhabitats (moss layer, gaps, Molinia caerulea tussocks). Using the extraction method, more seeds were found in the upper 0–3 cm soil layer than in the deeper 3–7 cm layer, significant differences in the number of seeds were found among microhabitats (with the lowest seed bank densities in Molinia tussocks). The highest number of seeds was found in the spring census, but the test was not significant (P<0.10). However, seasonal variation was found when damaged seeds were included in the analysis. Changes in damaged/undamaged and light/heavy seed ratios, and in numbers of grass/herbs/sedges seeds are also discussed. The spatial distribution of seeds is probably influenced to a great degree by abiotic factors, such as microtopography (round and heavy seeds of sedges prevail in gaps and in deeper soil layers). The species composition of the seed bank varied among microhabitats, depth, and throughout the year. No differences were found by the seed germination method.     

Seasonal changes in planktonic bacterial assemblages of two Ohio streams

1. Monthly water samples were collected from two Ohio streams (Bixon and Mahoning) for 14 months to assess the extent of seasonal changes in the bacterial assemblage and in a population within the assemblage. At the assemblage level, abundances of total bacteria and colony forming units (CFUs) were measured. Populations of Burkholderia ( Pseudomonas ) cepacia were quantified by colony hybridization using a species-specific rDNA probe.
2. Total bacterial numbers were highest in early winter and were lowest during summer and when the streams were covered with ice. Changes in the number of CFUs were more variable than changes in total number, but did not exhibit a clear seasonal pattern.
3. B. cepacia was not detected during summer, but up to 8000 ml^–1 were present in November. Seasonal changes in assemblage-level measurements were dissimilar to population-level changes in B. cepacia abundance.
4. The temporal changes observed in this study suggest that populations of stream bacteria, such as B. cepacia , exhibit seasonal blooms that are undetected by assemblage level measurements.     

Size diversity and species diversity relationships in fish assemblages of Western Palearctic lakes

Body size, coupled with abundance and taxonomy, may help to understand the mechanisms shaping community structure. Since the body size of fish is closely related to their trophic niche, size diversity (based on individual body size) of fish communities may capture intraspecific variations in fish trophic niches that are not detected by species diversity. Thus, the relationship between size diversity and species diversity may help to integrate variation at both intraspecific and interspecific levels. We studied the relationship between species diversity and size diversity as a measure of the degree of overlap in size among species and thereby the potential overlap in niches in a community. We hypothesized that the relationship between size diversity and species would be different across the European continent due to different levels of size overlap in fish communities. The data were derived from samplings of fish communities using standardised benthic gill nets in 363 lakes. At the continental scale, size diversity increased with species diversity; at the ecoregion scale, the slope of the relation changed across the continent, with the greatest mismatch occurring in northern Europe where communities comprised only one or a few species, but each of which exhibited a great range in size. There was an increase in slope towards the south with significant relations for four out of six ecoregions. The steeper size diversity‐species diversity slope at lower latitudes is attributable to a lower overlap in fish size and thus likely to finer niche separation. Our results also suggest that size diversity is not a strong surrogate for species diversity in European lake fish communities. Thus, particularly in fish communities composed of few species, measuring size diversity may help to detect potential functional variation which may be neglected by measuring species diversity alone.     

Seasonal changes in bird assemblages of coastal woodlands in east-central Argentina

We studied seasonal variation in bird assemblages during two years in the coastal woodlands of the reserve, 'El Destino', Buenos Aires Province, Argentina. Higher bird density was recorded during spring, and lower one during autumn, but species richness did not show changes during the annual cycle. Seasonal variation in abundance and species composition was recorded for the frugivore-insectivore and the granivore guilds, however, not for the insectivores. As winter is not harsh, insectivorous species might not be faced with food shortage. In contrast, the abundance of frugivorous-insectivorous and granivorous species appeared to be related with fluctuations in their food resources.     

Comparative analysis of bacterioplankton assemblages from maritime Antarctic freshwater lakes with contrasting trophic status

The bacterioplankton assemblages of eight maritime Antarctic lakes with a wide range of trophic status and geographic span (six lakes from Hope Bay, Antarctic Peninsula and two from Potter Peninsula, King George Island) were described using denaturing gradient gel electrophoresis and band sequencing during two consecutive austral summers (2003–2004). Analyses of the gels identified a total of 230 bands spread across 57 different positions. Among those bands, 14 were shared between lakes from Hope Bay and Potter Peninsula, 17 were observed only in particular lakes, and 17 were registered both years in the same lake. We successfully reamplified and sequenced 43 bands located in 36 different positions belonging to Bacteroidetes, Actinobacteria, Betaproteobacteria and Cyanobacteria. The closest matches for 63% of the sequenced bands were from Antarctic or from other cold environment clones and sequences already in the databases, suggesting the widespread dominance of microbial communities adapted to cold habitats. The results of the multivariate analyses (Cluster Analysis and CCA) indicated that the nutrient status of the lake influences the bacterioplankton assemblages. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Seasonal changes of Antarctic marine bacterioplankton and sea ice bacterial assemblages

The distributions of bacterial populations in sea ice and underlying seawater were investigated on the continental shelf of the “Terre Adélie” area. A reference station was sampled weekly from January 1991 to January 1992. In winter, the survey included a minimum of six sampling layers: surface and bottom ice, brine, seawater from the interface, and at 0.5 and 2 m depth. In seawater, the total bacterial abundance ranged from 0.5 × 10⁵ cells ml⁻¹ in July to 6.0 × 10⁵ cells ml⁻¹ after ice break. Values reaching 2.5 × 10⁶ cells ml⁻¹ were recorded in the overlying ice cover. Mean cell volumes were twice as high in brine as in seawater. The saprophytic bacterial abundance ranged from 5.0 × 10⁴ CFU (colony-forming units) ml⁻¹ in some winter interface samples to less than 1.0 × 10³ CFU ml⁻¹ in most of the summer seawater samples. In sea ice a clear decreasing gradient for most of the studied bacterial parameters from the surface layers towards the bottom layer was found. The ice cover had a discernible impact on underlying seawater, but its influence was restricted to a limited interface layer.     

Steady state phytoplankton assemblages during thermal stratification in deep alpine lakes. Do they occur?

Phytoplankton seasonal and long-term succession can be described and functionally classified by associations similar as in terrestrial vegetation studies. Such a concept has to include 'climax' into pelagic succession which in turn leads to the question to what extent steady state assemblages occur and if during periods of dynamic equilibrium can be identified. Here we explore the situation with respect to the above question for deep, nutrient poor, alpine lakes in Austria. We first track the long-term development of phytoplankton biomass, their taxonomic structure and their relation to total phosphorus and chlorophyll-a as predictors of trophic state over the past 35 years. We then analyse this data set for coherent algal associations which can be ascribed to trait separated functional groups according to Reynolds et al. (2002). A three year period of stable environmental conditions has then be extracted from the progression of trophic state indices, having similar dominating species each year. These years were finally analysed for steady state conditions according to definitions given in Sommer et al. (1993). During thermal stratification, achievement of an equilibrium could be ruled out although coexistence of several dominating species lasted for several weeks. Habitat templates were constructed from environmental variables prior to biomass peaks for two species important in summer assemblages, the dinoflagellate Ceratium hirundinella and the diatom Fragilaria crotonensis. In summary, functional groups proved to be a valid and useful concept to describe species succession of phytoplankton in deep alpine lakes while pelagic climax is much less clear and steady state conditions were never met.     

Effects of upstream lakes and nutrient limitation on periphytic biomass and nitrogen fixation in oligotrophic, subalpine streams

1. We conducted bioassays of nutrient limitation to understand how macronutrients and the position of streams relative to lakes control nitrogen (N₂) fixation and periphytic biomass in three oligotrophic Rocky Mountain catchments. We measured periphytic chlorophyll‐a (chl‐a) and nitrogen‐fixation responses to nitrogen (N) and phosphorus (P) additions using nutrient‐diffusing substrata at 19 stream study sites, located above and below lakes within the study catchments. 2. We found that periphytic chl‐a was significantly co‐limited by N and P at 13 of the 19 sites, with sole limitation by P observed at another four sites, and no nutrient response at the final two sites. On average, the addition of N, P and N + P stimulated chl‐a 35%, 114% and 700% above control values respectively. The addition of P alone stimulated nitrogen fixation by 2500% at five of the 19 sites. The addition of N, either with or without simultaneous P addition, suppressed nitrogen fixation by 73% at nine of the 19 sites. 3. Lake outlet streams were warmer and had higher dissolved organic carbon concentrations than inlet streams and those further upstream, but position relative to lakes did not affect chl‐a and nitrogen fixation in the absence of nutrient additions. Chl‐a response to nutrient additions did not change along the length of the study streams, but nitrogen fixation was suppressed more strongly by N, and stimulated more strongly by P, at lower altitude sites. The responses of chl‐a and nitrogen fixation to nutrients were not affected by location relative to lakes. Some variation in responses to nutrients could be explained by nitrate and/or total N concentration. 4. Periphytic chl‐a and nitrogen fixation were affected by nutrient supply, but responses to nutrients were independent of stream position in the landscape relative to lakes. Understanding interactions between nutrient supply, nitrogen fixation and chl‐a may help predict periphytic responses to future perturbations of oligotrophic streams, such as the deposition of atmospheric N.     

Epiphyton as a niche for ammonia-oxidizing bacteria: detailed comparison with benthic and pelagic compartments in shallow freshwater lakes

Next to the benthic and pelagic compartments, the epiphyton of submerged macrophytes may offer an additional niche for ammonia-oxidizing bacteria in shallow freshwater lakes. In this study, we explored the potential activities and community compositions of ammonia-oxidizing bacteria of the epiphytic, benthic, and pelagic compartments of seven shallow freshwater lakes which differed in their trophic status, distribution of submerged macrophytes, and restoration history. PCR-denaturing gradient gel electrophoresis analyses demonstrated that the epiphytic compartment was inhabited by species belonging to cluster 3 of the Nitrosospira lineage and to the Nitrosomonas oligotropha lineage. Both the ammonia-oxidizing bacterial community compositions and the potential activities differed significantly between compartments. Interestingly, both the ammonia-oxidizing bacterial community composition and potential activity were influenced by the restoration status of the different lakes investigated.     

Vertical foodweb structure of freshwater zooplankton assemblages estimated by stable nitrogen isotopes

Although theoretical foodweb models predict the presence of only three to four trophic categories, estimation of “potential” vertical foodweb structure from species lists and inferred feeding interactions suggest that as many as 7 trophic categories can occur in the pelagic foodwebs of North American glaciated lakes. A compilation of data on the nitrogen isotopic composition of zooplankton from 46 Canadian Shield lakes suggested the average existence of one “realized” trophic category in addition to that of filter-feeding, herbivorous cladocerans. When phytoplankton, planktivorous invertebrates, and plantivorous and piscivorous fish are included, the vertical foodweb structure in the pelagic zones of these lakes are greater than those hypothesized from some theoretical models.     

Review of ammonia-oxidizing bacteria and archaea in freshwater ponds

Aquaculture ponds are simple and unique ecosystems, which are affected intensively by human activities. In this mini-review, we focus our attention on the distribution and community diversity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in pond water and sediments, as well as the possible ecological mechanisms involved. Moreover, we discuss the possibility of increasing the activity of ammonia-oxidizing organisms in order to improve the water quality in aquaculture ponds. Compared with eutrophic lakes, the significantly higher ammonia concentration in pond water does not lead to significantly higher AOB levels, and the abundance of AOA is too low to quantify accurately. Similar to eutrophic lakes, high abundances of AOA and AOB are present in the surface sediments at the same time, where the oxidation of ammonia is performed mainly by AOB. AOB and AOA exhibit significant seasonal variations in aquaculture ponds, which are affected by the temperature, pH, and dissolved oxygen. The dominant AOB species are Nitrosomonas and the Nitrosospira lineage in pond environments. Nitrososphaera or members of the Nitrososphaera-like cluster dominate the AOA species in surface sediments, whereas the Nitrosopumilus cluster dominates the deeper sediments. AOB and AOA can be enriched on artificial substrates suspended in the pond water, thereby potentially improving the water quality.