Diversity and composition of bacterial community in the rhizosphere sediments of submerged macrophytes revealed by 454 pyrosequencing

Freshwater lake sediments support a variety of submerged macrophytes that may host groups of bacteria exerting important ecological functions. We collected three kinds of commonly found submerged macrophyte species (Ceratophyllum demersum, Vallisneria spiralis and Elodea nuttallii) to investigate the bacterial community associated with their rhizosphere sediments. High-throughput 454 pyrosequencing and bioinformatics analyses were performed to examine the diversity and composition of the bacterial community. The results obtained indicated that the diversity of the bacterial community associated with the rhizosphere sediments of submerged macrophytes was significantly lower than that of the bulk sediment. Remarkable differences in the bacterial community composition between the rhizosphere and bulk sediments were also observed.     

Comparative evaluation of anaerobic bacterial communities associated with roots of submerged macrophytes growing in marine or brackish water sediments

Sediment microbial communities are important for seagrass growth and carbon cycling, however relatively few studies have addressed the composition of prokaryotic communities in seagrass bed sediments. Selective media were used enumerate culturable anaerobic bacteria associated with the roots of the seagrass, Halodule wrightii, the fresh to brackish water plant, Vallisneria americana, and the respective vegetated and unvegetated sediments. H. wrightii roots and sediments had high numbers of sulfate-reducing bacteria whereas iron-reducing bacteria appeared to have a more significant role in V. americana roots and sediments. Numbers of glucose-utilizing but not acetate-utilizing iron reducers were higher on the roots of both plants relative to the vegetated sediments indicating a difference within the iron reducing bacterial community. H. wrightii roots had lower glucose-utilizing iron reducers, and higher acetogenic bacteria than did V. americana roots suggesting different aquatic plants support different anaerobic microbial communities. Sulfur-disproportionating and sulfide-oxidizing bacteria were also cultured from the roots and sediments. These results provide evidence of the potential importance of sulfur cycle bacteria, in addition to sulfate-reducing bacteria, in seagrass bed sediments.     

Effects of two common macrophytes on methane dynamics in freshwater sediments

The methane cycle in constructed wetlands without plants and withPhragmites australis (reed) and Scirpus lacustris (bulrush) wasinvestigated. Variations in CH₄production largely determined variations in CH₄ emission among the systems, rather than variations inCH₄ storage and oxidation. Twofoldlower CH₄ production rates in theScirpus system (5.6–13 mmol m^-2 d^-1) relative to the control (16.7–17.6 mmolm^-2 d^-1) were accompanied by a lower contribution ofmethanogenesis to organic carbon metabolism (20% for Scirpus vs.80% for control). Sedimentary iron(II) reservoirs were smallerin the Scirpus than control sediment (300 vs. 485 mmol.m^-2) and a shuttle role for iron asan intermediate between root O₂release and carbon oxidation, attenuating the availability of substrate formethanogens, is suggested. Differences in CH₄ production among the Phragmites and Scirpus systemswere controlled by the interspecific variation in sediment oxidationcapacities of both plant species. Comparatively, in the Phragmites sediment,dissolved iron reservoirs were larger (340 mmol.m^-2) and methanogenesis was a more importantpathway (80%). Methane transport was mainly plant mediated inthe Phragmites and Scirpus systems, but ebullition dominated in thenon-vegetated control systems as well as in the vegetated systems when plantbiomass was low.     

Epiphytic algae and macroinvertebrates on submerged and floating-leaved macrophytes in an Italian lake

1. The presence of contiguous beds of submerged (Myriophyllum spicatum, Ceratophyllum demersum and Najas marina) and floating-leaved (Trapa natans) vegetation in a north Italian lake allowed us to test the effect of the different host architecture on epiphytic algae and invertebrates and to predict the consequences for the lake of changes in the predominant vegetation. 2. Epiphyton development, measured as carbon, nitrogen, phosphorus, chlorophyll a (Chl a), phaeophytin and as algal and macroinvertebrate density, was significantly higher on submerged plants than on T. natans. The C : Chl a ratio, a proxy of the ratio of heterotrophs to autotrophs, was higher on the floating-leaved plants. The elemental (C : N : P) and pigment (Chl a : phaeophytin) ratios were not significantly different between the two vegetation types. 3. The taxonomic composition of epiphytic algae and invertebrates was similar on the different plants. The more varied morphology of the floating-leaved T. natans resulted in a higher diversity of epiphytic algae, however, but not of macroinvertebrates. 4. There was a significant inverse relationship between epiphyton biomass and the standing crop of the host plant, suggesting a key role for light and water exchange in epiphyton development. 5. Replacement of floating-leaved by submerged plants would increase the total biomass of epiphytic algae and invertebrates.     

两种沉水植物对间隙水磷浓度的影响

为研究两种根系特征的沉水植物在生长过程中对间隙水中磷浓度的影响,选取根系较多的沉水植物苦草和根系相对较少的沉水植物黑藻作为实验材料,监测底泥中间隙水各形态磷含量及环境因子的变化,探讨不同根系特征沉水植物对间隙水中磷的影响。结果表明:黑藻和苦草实验组沉积物间隙水中各形态磷的浓度均呈不同程度的降低,黑藻和苦草对于稳定水质,减少底泥中磷向水中转移具有明显的效果;沉水植物不同,底泥间隙水中溶解性总磷(DTP)和溶解性活性磷(SRP)存在明显差异。实验结束时黑藻组和苦草组间隙水中DTP的浓度分别为0.24,0.01 mg/L,SRP的浓度分别为0.22 mg/L,0.004 mg/L。间隙水中磷的形态主要以DTP和SRP为主,溶解性有机磷(DOP)的含量相对较低。沉水植物对间隙水中磷的吸收是降低间隙水中磷含量的重要原因,苦草的吸收能力大于黑藻。沉水植物根系通过降低底泥p H值,提高氧化还原电位(Eh)的方式抑制了底泥中磷的释放。     

Functional traits composition predict macrophytes community productivity along a water depth gradient in a freshwater lake

Functional trait composition of plant communities has been proposed as a helpful key for understanding the mechanisms of biodiversity effects on ecosystem functioning. In this study, we applied a step‐wise modeling procedure to test the relative effects of taxonomic diversity, functional identity, and functional diversity on macrophytes community productivity along water depth gradient. We sampled 42 plots and 1513 individual plants and measured 16 functional traits and abundance of 17 macrophyte species. Results showed that there was a significant decrease in taxonomic diversity, functional identity (i.e., stem dry mass content, leaf [C] and leaf [N]), and functional diversity (i.e., floating leaf, mean Julian flowering date and rooting depth) with increasing water depth. For the multiple‐trait functional diversity (FD) indices, functional richness decreased, while functional divergence increased with water depth gradient. Macrophyte community productivity was strongly determined by functional trait composition within community, but not significantly affected by taxonomic diversity. Community‐weighted means (CWM) showed a two times higher explanatory power relative to FD indices in determining variations in community productivity. For nine of sixteen traits, CWM and FD showed significant correlations with community productivity, although the strength and direction of those relations depended on selected trait. Furthermore, functional composition in a community affected productivity through either additive or opposite effects of CWM and FD, depending on the particular traits being considered. Our results suggested both mechanisms of mass ratio and niche complementarity can operate simultaneously on variations in community productivity, and considering both CWM and FD would lead to a more profound understanding of traits–productivity relationships.     

Phosphorus chemistry and bacterial community composition interact in brackish sediments receiving agricultural discharges

Background

External nutrient discharges have caused eutrophication in many estuaries and coastal seas such as the Baltic Sea. The sedimented nutrients can affect bacterial communities which, in turn, are widely believed to contribute to release of nutrients such as phosphorus from the sediment.

Methods

We investigated relationships between bacterial communities and chemical forms of phosphorus as well as elements involved in its cycling in brackish sediments using up-to-date multivariate statistical methods. Bacterial community composition was determined by terminal restriction fragment length polymorphism and cloning of the 16S rRNA gene.

Results and Conclusions

The bacterial community composition differed along gradients of nutrients, especially of different phosphorus forms, from the estuary receiving agricultural phosphorus loading to the open sea. This suggests that the chemical composition of sediment phosphorus, which has been affected by riverine phosphorus loading, influenced on bacterial communities. Chemical and spatial parameters explained 25% and 11% of the variation in bacterial communities. Deltaproteobacteria, presumptively sulphate and sulphur/iron reducing, were strongly associated to chemical parameters, also when spatial autocorrelation was taken into account. Sulphate reducers correlated positively with labile organic phosphorus and total nitrogen in the open sea sediments. Sulphur/iron reducers and sulphate reducers linked to iron reduction correlated positively with aluminium- and iron-bound phosphorus, and total iron in the estuary. The sulphate and sulphur/iron reducing bacteria can thus have an important role both in the mineralization and mobilization of nutrients from sediment.

Significance

Novelty in our study is that relationships between bacterial community composition and different phosphorus forms, instead of total phosphorus, were investigated. Total phosphorus does not necessarily bring out interactions between bacteria and phosphorus chemistry since proportions of easily usable mobile (reactive) phosphorus and immobile phosphorus forms in different sediments can vary. Our study suggested possible feedbacks between different forms of phosphorus and bacterial community composition.     

Changes in freshwater bacterial community composition during measurements of microbial and community respiration

The respiration rates of a pelagic community and of its microbialfraction (< 1.2 µm) were measured at two depths inthe oxic layer of a meromictic alpine lake (Cadagno, Switzerland)using the oxygen technique. The duration of the incubationswere 12, 24 and 55 h. Bacterioplankton abundance (DAPI counts)and composition (whole cell hybridization using 11 group-specificrRNA-targeted oligonucleotide probes) were measured during theincubations. Respiration generally increased with time, especiallyin the microbial fraction, or remained similar. This resultwas not always consistent with changes in bacterial abundanceand cell volume. The composition of the community also changedduring the incubations. The abundance of ß-Proteobacteriaincreased during the course of all the experiments. These resultsextend the previous conclusions drawn in marine environmentsto fresh waters and demonstrate that, in addition to changesin bacterial abundance, cell volume and biomass, changes inthe taxonomic composition of the bacterial community can occurduring discrete incubations of freshwater planktonic communities.     

Epiphytic diatoms in two freshwater maritime Antarctic lakes

SUMMARY.

• 1 An ecological study of two small maritime Antarctic lakes on Signy Island, South Orkney Islands, was undertaken from January 1986 to March 1987. Analysis of diatom counts from the lakes provided examples of oligotrophic and mesotrophic ecosystems.
• 2 A diverse community of 104 epiphytic taxa was identified. Twenty-eight taxa had a percentage abundance greater than 1% in both lakes. Distinctive dominant taxa were identified from each lake.
• 3 A variety of ordination techniques was performed on the abundance data and a principal components analysis demonstrated differences in the diatom assemblages between the two lakes. Clear separations of sites and species were evident between the lakes, and accounted for the greatest percentage variance.
• 4 Species composition varied with depth within each lake and was also important in influencing changes in assemblage composition between sites.
• 5 A redundancy analysis indicated that species composition was correlated to concentrations of nitrogen and phosphorus but the total variance accounted for by the four physical and chemical factors measured was low (24%).

     

The influence of habitat heterogeneity on freshwater bacterial community composition and dynamics

Multiple forces structure natural microbial communities, but the relative roles and interactions of these drivers are poorly understood. Gradients of physical and chemical parameters can be especially influential. In traditional ecological theory, variability in environmental conditions across space and time represents habitat heterogeneity, which may shape communities. Here we used aquatic microbial communities as a model to investigate the relationship between habitat heterogeneity and community composition and dynamics. We defined spatial habitat heterogeneity as vertical temperature and dissolved oxygen (DO) gradients in the water column, and temporal habitat heterogeneity as variation throughout the open-water season in these environmental parameters. Seasonal lake mixing events contribute to temporal habitat heterogeneity by destroying and re-creating these gradients. Because of this, we selected three lakes along a range of annual mixing frequency (polymictic, dimictic, meromictic) for our study. We found that bacterial community composition (BCC) was distinct between the epilimnion and hypolimnion within stratified lakes, and also more variable within the epilimnia through time. We found stark differences in patterns of epilimnion and hypolimnion dynamics over time and across lakes, suggesting that specific drivers have distinct relative importance for each community.     

Fine-scale spatial patterns in bacterial community composition and function within freshwater ponds

The extent to which non-host-associated bacterial communities exhibit small-scale biogeographic patterns in their distribution remains unclear. Our investigation of biogeography in bacterial community composition and function compared samples collected across a smaller spatial scale than most previous studies conducted in freshwater. Using a grid-based sampling design, we abstracted 100+ samples located between 3.5 and 60 m apart within each of three alpine ponds. For every sample, variability in bacterial community composition was monitored using a DNA-fingerprinting methodology (automated ribosomal intergenic spacer analysis) whereas differences in bacterial community function (that is, carbon substrate utilisation patterns) were recorded from Biolog Ecoplates. The exact spatial position and dominant physicochemical conditions (for example, pH and temperature) were simultaneously recorded for each sample location. We assessed spatial differences in bacterial community composition and function within each pond and found that, on average, community composition or function differed significantly when comparing samples located >20 m apart within any pond. Variance partitioning revealed that purely spatial variation accounted for more of the observed variability in both bacterial community composition and function (range: 24–38% and 17–39%) than the combination of purely environmental variation and spatially structured environmental variation (range: 17–32% and 15–20%). Clear spatial patterns in bacterial community composition, but not function were observed within ponds. We therefore suggest that some of the observed variation in bacterial community composition is functionally ‘redundant''. We confirm that distinct bacterial communities are present across unexpectedly small spatial scales suggesting that populations separated by distances of >20 m may be dispersal limited, even within the highly continuous environment of lentic water.     

Investigation of total bacterial and ammonia-oxidizing bacterial community composition in a full-scale aerated submerged biofilm reactor for drinking water pretreatment in China

The community composition of total bacteria and ammonia-oxidizing bacteria in a full-scale aerated submerged biofilm reactor for drinking water pretreatment was characterized by analysis of 16S rRNA gene and the functional gene amoA, respectively. Sampling was performed in February and in July. 16S rRNA gene clone libraries revealed 13 bacterial divisions. At both sampling dates, the majority of clone sequences were related to the Alpha- and Betaproteobacteria. A minor proportion belonged to the following groups: Gammaproteobacteria, Deltaproteobacteria, Nitrospira, Firmicutes, Acidobacteria, Verrucomicrobia, Actinobacteria, Planctomycetes, Chloroflexi, Gemmatimonadetes and the Cytophaga-Flavobacterium-Bacteroides group. Some sequences related to bacteria owning high potential metabolic capacities were detected in both samples, such as Rhodobacter-like rRNA gene sequences. Surveys of cloned amoA genes from the two biofilm samples revealed ammonia-oxidizing bacterial sequences affiliated with the Nitrosomonas oligotropha lineage, Nitrosomonas communis lineage. An unknown Nitrosomonas group of amoA gene sequences was also detected.     

Changes in functional composition and diversity of waterbirds: The roles of water level and submerged macrophytes

1. Water level and submerged macrophytes are critical players for the functioning of shallow lake ecosystems; understanding how waterbird communities respond to changes in both can have important implications for conservation and management. Here, we evaluated the effects of changes in water level and submerged macrophyte status on wintering waterbird community size, functional group abundances, functional diversity (FD), and community assembly by using a dataset compiled over 50 years.
2. We built generalised linear models to evaluate the effects of water level and submerged macrophyte status on the above-listed attributes of the waterbird communities by using mid-winter waterbird censuses, water level measurements, and submerged macrophyte surveys, along with submerged macrophyte macrofossil records from two shallow lakes in Turkey. Using a relevant set of functional traits, we defined functional groups, calculated four FD measures, and simulated null distributions of the FD measures for assessing assembly rules.
3. We found that macrophyte-dominated years had significantly higher abundances of waterbirds in one of the study lakes, and had more diving herbivores and omnivores in both lakes, while diving/scooping fish-eating waterbird abundance was lower in macrophyte-dominated years. Community size in Lake Beyşehir exhibited a negative association with water level; surprisingly, however, none of the functional group abundances and FD indices were significantly related to water level.
4. In our study communities, standardised effect sizes of functional richness and functional dispersion—two indices that are particularly sensitive to community assembly processes—were mostly lower than those of randomly assembled communities, which implies functional clustering. Shifts to a scarce-macrophyte state were associated with increases in these two indices, possibly due to either changes in the relative strength of environmental filtering and limiting similarity in community assembly or sampling of transitional communities. Further studies covering a wider range of the trophic/macrophyte status spectrum are needed to be certain.
5. The results of this study indicate that shifts between abundant and scarce-macrophyte states can have significant effects on wintering waterbird abundances, FD and community assembly. The results also suggest that shallow lakes in macrophyte-dominated states can support more wintering waterbirds, especially diving omnivores, some of which are globally threatened.

     

Influences of light and temperature on chlorophyll composition in submersed freshwater macrophytes

In three submersed freshwater macrophyte species grown in a greenhouse over broad experimental ranges of light and water temperature, total chlorophyll (a + b) increased with decreasing irradiance and, in two of the three species, with increasing temperature. In contrast, light and temperature had only minor and inconsistent influences on chlorophyll a : b in these species.From results of this and other investigations involving experimentally-controlled light conditions, it appears that total chlorophyll in submersed macrophytes is inversely related to irradiance above photon flux densities minimally required for plant growth. However, the general applicability of this statement to the species investigated here (or others) is uncertain, because thermal gradients in macrophyte dominated littoral zones may promote gradients in macrophyte total chlorophyll with depth in a direction opposite to that expected solely in response to light.     

Influence of submerged macrophytes on sediment composition and near-bed flow in lowland streams

1. Submerged macrophytes have important physical and structural effects on lowland streams. This study investigated the ability of submerged macrophytes to modify the near-bed flow and to retain mineral and organic particles in patches of four common macrophytes in shallow Danish streams during mid-summer. 2. In dense patches of Callitriche cophocarpa and Elodea canadensis, where near-bed velocity was reduced, the sediment surface was markedly raised and enriched with fine particles. In dense patches of Ranunculus peltatus, fine sediments were deposited among rooted shoots in the upstream part of the patches, while erosion and coarse sediments prevailed in the downstream part of the patches because of the strong vortices that formed at the rear and moved up under the trailing canopy. The open canopy of Sparganium emersum, with its streamlined leaves, had little effect on flow and sediment. 3. Patterns of sediment deposition and composition were closely related to the morphology and canopy structure of plant species and the presence of low velocity above the sediment among the rooted shoots. The mineral particles retained probably originate from bed-load, and the enrichment with finer particles within the patches probably results mainly from size-selective processes during erosion and transport of particles rather than during deposition. The mixed sediment composition within patches suggests that the flow-resistant shoots generate an environment conducive to deposition of all transported particles. 4. Fine sediments within macrophyte beds contained high concentrations of organic matter, carbon, nitrogen and phosphorus. The wide scatter in the relationships between mineral grain size and the content of organic matter and nutrients reflects the spatial and temporal complexity of erosion, transport and sedimentation of mineral and organic particles. 5. Enrichment of sediment within macrophyte beds relative to the surrounding substratum ranged from 780 g organic matter m^–2, 30 g N m^–2 and 25 g P m^–2 for the flow-resistant dense canopies af Callitriche cophocarpa to 150 g organic matter m^–2, 6.6 g N m^–2 and 3.4 g P m^–2 for the open canopies of Sparganium emersum. Retention of nutrient-rich particles within the macrophyte beds is probably of limited importance for plant growth in most lowland European streams, because macrophyte growth is rarely nutrient limited.     

Altering the balance between bacterial production and protistan bacterivory triggers shifts in freshwater bacterial community composition

Bacterivorous protists are known to induce changes in bacterial community composition (BCC). We hypothesized that changes in BCC could be related quantitatively to a measure of grazing: the ratio of bacterial mortality to growth rate. To test this hypothesis, we analyzed time-course changes in BCC, protistan grazing rate, and bacterial production from 3 in situ studies conducted in a freshwater reservoir and three laboratory studies. In the field experiments, samples were manipulated to yield different levels of protistan bacterivory and incubated in dialysis bags. Laboratory investigations were continuous cultivation studies in which different bacterivorous protists were added to bacterial communities. BCC was assessed using 4–6 different rRNA-targeted oligonucleotide probes for community analysis. Change in BCC (Δ BCC) was estimated as the sum of changes in the proportions of the two phylogenetic groups that showed the largest shifts. Analysis of a set of 22 estimates of shifts in the ratio of grazing to production rate over periods of 48–72 h and Δ BCC showed that Δ BCC was positively and tightly correlated (r ² = 0.784) with shifts in the ratio of grazing mortality to cell production. While the nature of a shift in BCC is unpredictable, the magnitude of the change can be related to changes in the balance between bacterial production and protistan grazing. This revised version was published online in August 2006 with corrections to the Cover Date.     

沉水植物附着细菌群落结构及其多样性研究进展

与陆生植物类似,沉水植物的叶表也存在着大量的附着细菌。附着细菌拥有独特的生态位和显著的生态功能,与沉水植物构成了复杂的共生体系。针对附着细菌的群落结构及其多样性进行了简单的综述。在方法学上,"表面活性剂+超声处理"的方式能够比较有效地洗脱叶表的附着细菌。显微计数和分离培养的方法分别发现,某些沉水植物附着细菌的多度在105~107个/cm2以及106 CFU/cm左右。克隆测序的研究表明沉水植物附着细菌的OTU在几十到上百的范围内。在群落结构上,Betaproteobacteria、Bacteroidetes、Alphaproteobacteria、Actinobacteria、Planctomycetes、Cyanobacteria等门类的细菌较为常见。先锋物种在附着细菌生物膜的形成过程中发挥着关键作用,环境条件和植物体都会对附着细菌的多样性造成影响。富营养化水体观察到较高的附着细菌丰度,溶解性有机物比无机营养物更加适合附着细菌的利用。植物体的叶片化学组成、渗出物以及物理结构等会影响附着细菌的多样性及群落结构。对沉水植物附着细菌群落结构形成的机理进行了假说性质的总结,并对附着细菌的研究前沿进行了展望。     

Effects of substrate and shading on the growth of two submerged macrophytes

Excessive nutrient loading may cause a shift from submerged macrophyte dominance to free-floating macrophyte dominance. Tolerance and persistence of submerged plants in response to shade may be key characteristics in determining when/if such a shift occurs in shallow eutrophic lakes. This study examines how the cover of floating macrophyte (Lemna minor) and shade of dark mesh affect the growth and photosynthetic efficiency of two submerged plants (Vallisneria natans and Myriophyllum spicatum) on different nutrient substrates. We found that low- and mid-cover intensities generally enhanced the leaf/shoot growth of both submerged plants under all cover and substrate types. The relative growth rates (RGR) were slightly enhanced under the treatment of Lemna with low- and mid-intensity cover on both nutrient-rich substrates. The leaf/shoot growth and RGR of both submerged macrophytes generally increased more under Lemna cover than mesh cover. The photosynthetic efficiency (F _v/F _m value) typically increased with the duration of treatment and the cover densities. In addition, these two macrophytes with contrasting growth forms have markedly different growth and survival strategies in response to covers. These results strengthen the hypothesis that submerged plants can successfully develop under a low-intensity cover of floating vegetation on nutrient-rich substrate.