Use of phytoplankton-derived dissolved organic carbon by different types of bacterioplankton

Phytoplankton and heterotrophic prokaryotes are major components of the microbial food web and interact continuously: heterotrophic prokaryotes utilize the dissolved organic carbon derived from phytoplankton exudation or cell lysis (DOCp), and mineralization by heterotrophic prokaryotes provides inorganic nutrients for phytoplankton. For this reason, these communities are expected to be closely linked, although the study of the interactions between them is still a major challenge. Recent studies have presented interactions between phytoplankton and heterotrophic prokaryotes based on coexistence or covariation throughout a time-series. However, a real quantification of the carbon flow within these networks (defined as the interaction strength, IS) has not been achieved yet. This is critical to understand the selectivity degree of bacteria responding to specific algal DOCp. Here we used microautoradiography to quantify the preferences of the major heterotrophic prokaryote phylogenetic groups on DOC derived from several representative phytoplankton species, and expressed these preferences as an IS value. The distribution of the ISs was not random but rather skewed towards weak interactions, in a similar way as the distributions described for stable complex non-microbial ecosystems, indicating that there are some cases of high specificity on the use of specific algal DOCp by some bacterial groups, but weak interactions are more common and may be relevant as well. The variety of IS patterns observed supports the view that the vast range of different resources (different types of organic molecules) available in the sea selects and maintains the high levels of diversity described for marine bacterioplankton.     

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.     

Limitation of lowland riverine bacterioplankton by dissolved organic carbon and inorganic nutrients

Flow regulation in lowland rivers has reduced the amount of allochthonous dissolved organic carbon (DOC) entering main channels through less frequent wetting of benches, flood runners and floodplains. The hypothesis tested was that lowland riverine bacterioplankton are DOC limited when flow events are absent and simulating an increase in assimilable DOC similar to that expected during an environmental flow will lead to heterotrophic dominance. Experiments took place in the Namoi River, a highly regulated lowland river in Australia. Specifically, in situ microcosms were used to examine the responses of bacterioplankton and phytoplankton to various additions of DOC as glucose or leaf leachate, with and without additions of inorganic nutrients. The results indicated that ambient DOC availability limited the bacterioplankton for the three seasons over which we conducted the experiments. When DOC was added alone, dissolved oxygen concentrations decreased primarily because of increased bacterial respiration and bacterioplankton growth generally increased relative to controls. Additions of DOC alone led to a pattern of decreased chlorophyll a concentration relative to controls, except for willow leachate. Additions of inorganic nutrients alone increased chlorophyll a concentrations above controls, indicating limitation of phytoplankton. These findings support our hypothesis. Based on the present results, environmental flows should increase the duration of allochthonously driven heterotrophic dominance, thus shifting regulated lowland rivers to more natural (pre-regulation) conditions for greater periods.     

Transporter genes expressed by coastal bacterioplankton in response to dissolved organic carbon

Coastal ocean bacterioplankton control the flow of dissolved organic carbon (DOC) from terrestrial and oceanic sources into the marine food web, and regulate the release of inorganic carbon to atmospheric and offshore reservoirs. While the fate of the chemically complex coastal DOC reservoir has long been recognized as a critical feature of the global carbon budget, it has been problematic to identify both the compounds that serve as major conduits for carbon flux and the roles of individual bacterioplankton taxa in mediating that flux. Here we analyse random libraries of expressed genes from a coastal bacterial community to identify sequences representing DOC‐transporting proteins. Predicted substrates of expressed transporter genes indicated that carboxylic acids, compatible solutes, polyamines and lipids may be key components of the biologically labile DOC pool in coastal waters, in addition to canonical bacterial substrates such as amino acids, oligopeptides and carbohydrates. Half of the expressed DOC transporter sequences in this coastal ocean appeared to originate from just eight taxa: Roseobacter, SAR11, Flavobacteriales and five orders of γ‐Proteobacteria. While all major taxa expressed transporter genes for some DOC components (e.g. amino acids), there were indications of specialization within the bacterioplankton community for others (e.g. carbohydrates, carboxylic acids and polyamines). Experimental manipulations of the natural DOC pool that increased the concentration of phytoplankton‐ or vascular plant‐derived compounds invoked a readily measured response in bacterial transporter gene expression. This highly resolved view of the potential for carbon flux into heterotrophic bacterioplankton cells identifies possible bioreactive components of the coastal DOC pool and highlights differing ecological roles in carbon turnover for the resident bacterial taxa.     

Distribution of dissolved organic carbon in lakes of different trophic types

The distributions of dissolved organic carbon (DOC) in the warm season were elucidated in ten lakes of different trophic types in Japan, Russia, and China. DOC showed similar vertical distributions in all the lakes in summer when thermal stratification occurred. DOC in the epilimnion was higher than the value of 0.8mgCl^–1 found in the hypolimnion. In three Japanese lakes, hypolimnion DOC was negatively correlated with apparent oxygen utilization (AOU), reflecting the net oxidation of DOC using the dissolved oxygen in lake water. The DOC:O₂ ratios (0.115–0.179), calculated by the slopes of the regression lines of DOC versus AOU in hypolimnion water, were as low as those of deep-sea water, which indicates low bioavailability of lake water DOC for heterotrophic bacteria. DOC and conductivity did not correlate well except in two Japanese lakes: one showed a positive correlation and the other a negative correlation, indicating DOC loading from the inflowing rivers. Eutrophic lakes tended to have higher DOC values than meso- and oligotrophic lakes, and DOC values in the surface water negatively correlated with Secchi depths.     

亚热带不同稻田土壤溶解性有机碳的剖面分布特征

通过选取亚热带5种不同母质发育的稻田土壤(黄泥田Ⅰ、黄泥田Ⅱ、麻砂泥、红黄泥、河沙泥),按土壤发生层次采集剖面样品,研究土壤溶解性有机碳(DOC)的剖面分布特征及其与土壤有机碳(SOC)的关系,并探讨DOC的剖面迁移规律及影响因素.结果表明:稻田土壤剖面DOC含量介于13.61 ～90.34 mg · kg-1,以耕作层(A/Aa和Ap)最高,平均达到69.40 mg·kg-1,耕作层以下相对较低.除河沙泥外,其余4种稻田土壤剖面DOC含量并未随土层深度的增加而逐渐降低,而是在渗育层(P)及以下的某些土层(如We/W2层、C层)出现DOC含量较上一层次升高的现象.这可能与稻田土壤剖面特殊的DOC淋溶和淀积、生物降解、矿物相吸附和氧化还原状况有关.DOC/SOC的比例介于0.21％～1.31％,以耕作层土壤最低,表下层土壤相对较高,反映稻田表下层土壤SOC的活性较耕作层明显增强,在人为干扰(如翻耕)下,表下层土壤SOC可能更容易损失.相关分析表明,DOC与SOC呈显著正相关,剖面SOC含量对DOC的剖面分布具有决定作用.从维持土壤质量和固碳减排的角度看,应针对不同类型稻田土壤采取不同的耕作和管理措施.     

Simultaneous consumption and production of fluorescent dissolved organic matter by lake bacterioplankton

Recent evidence suggests a key role of bacterioplankton in shaping the composition of the dissolved organic matter (DOM) pool in aquatic systems, not only through consumption but also through production of specific compounds, but the latter process is still not well understood. We used a bioassay approach to assess the patterns in bacterial production and consumption of five fluorescent DOM pools in seven lakes and two streams in Southeastern Québec, Canada, and the links these patterns may have with key aspects of bacterial metabolism, DOM origin and nutrients availability. Total dissolved organic C declined by 3-15% during these incubations, whereas the specific DOM pools had very different dynamics: Two humic-like fractions accumulated in all incubations, with rates of production increasing as a function of bacterial growth efficiency, which itself increased with phosphorus concentrations. In contrast, two protein-like fractions and a third humic-like fraction either increased or declined over the course of the experiments. The net production or consumption of these pools appeared to be a function of the contribution of terrestrial C to bulk DOM (derived from δ(13) C of the DOM) and of total bacterial activity. Our results suggest that lake bacterioplankton play a dual role in DOM dynamics, as consumers and also producers, and that the interplay between DOM origin and nutrient availability appears to determine the net outcome of bacterial DOM processing, thus influencing the bulk DOM composition and its fate in these aquatic systems.     

Role of ultraviolet-B radiation on bacterioplankton and the availability of dissolved organic matter

Attenuation of ultraviolet (UV)-radiation into the water column is highly correlated with the concentration of the dissolved organic matter (DOM). Thus UV penetrates deeper into marine waters than into freshwater systems. DOM is efficiently cleaved by solar surface radiation levels consuming more oxygen than bacterial metabolism. This photolytically cleaved DOM exhibits higher absorbance ratios (250/365 nm) than untreated DOM. Natural bacterioplankton reach higher abundance if inoculated in previously solar-exposed DOM than in untreated DOM; during bacterial growth the absorbance ratio declines steadily indicating the utilization of the photolytically cleaved DOM. On the other hand, bacterioplankton are greatly reduced in their activity if exposed to surface solar radiation levels. Photoenzymatic repair of DNA induced by UV-A radiation, however, leads to an efficient recovery of bacterial activity once the UV-B stress is released. Turbulent mixing of the upper layers of the water column leads to a continuous alteration of the UV exposure regime. Close to the surface, bacteria and DOM are exposed to high levels of UV-B leading to a reduction in bacterial activity and to photolysis of DOM. Once mixed into deeper layers where UV-B is attenuated, but sufficient UV-A is remaining to allow photoenzymatic repair, the photolytically cleaved DOM is efficiently taken up by bacterioplankton leading to even higher bacterial activity than prior to the exposure. Thus, the overall effect of UV on bacterioplankton is actually an enhancement of bacterial activity despite their lack of protective pigments.     

Controls on fluxes and export of dissolved organic carbon in grasslands with contrasting soil types

Export of dissolved organic carbon (DOC) from grassland ecosystems can be an important C flux which directly affects ecosystem C balance since DOC is leached from the soil to the groundwater. DOC fluxes and their controlling factors were investigated on two grassland sites with similar climatic conditions but different soil types (Vertisol vs. Arenosol) for a 2.5-year period. Parts of both grasslands were disturbed by deep ploughing during afforestation. Contrary to what was expected, ploughing did not increase DOC export but surface soil DOC concentrations decreased by 28% (Vertisol) and 14% (Arenosol). DOC flux from the soil profile was negatively influences by the clay content of the soil with seven times larger DOC export in the clay-poor Arenosol (55 kg C ha^?1 a^?1) than in the clay-rich Vertisol (8 kg C ha^?1 a^?1). At the Arenosol site, highest DOC concentrations were measured in late summer, whereas in the Vertisol there was a time lag of several months between surface and subsoil DOC with highest subsoil DOC concentrations during winter season. DOC export was not correlated with soil organic carbon stocks. Large differences in ¹⁴C concentrations of 22–40 pMC between soil organic carbon and DOC in the subsoil indicated that both C pools are largely decoupled. We conclude that DOC export at both sites is not controlled by the vegetation but by physicochemical parameters such as the adsorption capacity of soil minerals and the water balance of the ecosystem. Only in the acidic sandy Arenosol DOC export was a significant C flux of about 8% of net ecosystem production.     

Community differentiation and population enrichment of Sargasso Sea bacterioplankton in the euphotic zone of a mesoscale mode‐water eddy

Eddies are mesoscale oceanographic features (～ 200 km diameter) that can cause transient blooms of phytoplankton by shifting density isoclines in relation to light and nutrient resources. To better understand how bacterioplankton respond to eddies, we examined depth‐resolved distributions of bacterial populations across an anticyclonic mode‐water eddy in the Sargasso Sea. Previous work on this eddy has documented elevated phytoplankton productivity and diatom abundance within the eddy centre with coincident bacterial productivity and biomass maxima. We illustrate bacterial community shifts within the eddy centre, differentiating populations uplifted along isopycnals from those enriched or depleted at horizons of enhanced bacterial and primary productivity. Phylotypes belonging to the Roseobacter, OCS116 and marine Actinobacteria clades were enriched in the eddy core and were highly correlated with pigment‐based indicators of diatom abundance, supporting developing hypotheses that members of these clades associate with phytoplankton blooms. Typical mesopelagic clades (SAR202, SAR324, SAR406 and SAR11 IIb) were uplifted within the eddy centre, increasing bacterial diversity in the lower euphotic zone. Typical surface oligotrophic clades (SAR116, OM75, Prochlorococcus and SAR11 Ia) were relatively depleted in the eddy centre. The biogeochemical context of a bloom‐inducing eddy provides insight into the ecology of the diverse uncultured bacterioplankton dominating the oligotrophic oceans.     

Seasonal variation of particulate organic carbon, dissolved organic carbon and the contribution of microbial communities to the live particulate organic carbon in a shallow near-bottom ecosystem at the Northwestern Mediterranean Sea

Microbial planktonic communities (i.e. bacteria and protozoa), phytoplankton, dissolved organic carbon (DOC) and particulate organic carbon (POC) were seasonally examined at Medes Islands (Northwestern Mediterranean) to assess their variation in abundance and composition throughout the year in a near-bottom littoral ecosystem. From October 1995 to November 1996, samples were collected between two and six times per month at 0.5 m above the bottom. Mean DOC and POC values throughout the year were 2560 180 (SE) and 387 ± 35 g C l^-1, respectively. All year, detrital organic carbon (detrital=total POC - live carbon) represented the main POC fraction, and mean live carbon was 24 ± 9 g C l^-1. Winter and spring had maximum values of POC, and spring and summer had maximum values of DOC. Heterotrophic bacteria, with a mean abundance of 5.16 ± 0.08 x 10⁵ cells ml^-1, were the main contributor to live carbon (26 ± 7%). During winter, heterotrophic bacterial biomass decreased 40% due to a decrease in mean biovolume per cell. Synechococcus sp. and Prochlorococcus sp. abundance were 2.24 ± 0.09 x 10⁴ and 1.05 ± 0.07 x 10⁴ cells ml^-1, respectively. However, while Synechococcus sp. were present all year, Prochlorococcus sp. were not observed from April to July. Mean phytoplankton (i.e. diatoms and dinoflagellates) abundance was 2.06 ± 0.40 x 10⁴ cells l^-1 with biomass at a maximum during the winter months, the period with the lowest temperature and the highest nutrient concentration. The size composition of live carbon showed two clearly distinct periods: from December to March, live carbon was dominated in biomass by microplankton, while from April to November, pico- and nanoplankton cells were dominant. Overall, the dynamics of the near-bottom planktonic communities was characterized by a low biomass of heterotrophic and autotrophic bacteria, phytoplankton and ciliates in contrast to previous water column studies. This pattern and the high temporal heterogeneity of the different planktonic communities are discussed in relation to the physical and chemical characteristics of the environment, as well as to the potential role that benthic communities may be exerting in the control of the near-bottom planktonic communities.      

Effective isolation of bacterioplankton genus Polynucleobacter from freshwater environments grown on photochemically degraded dissolved organic matter

Effective isolation of freshwater bacterioplankton belonging to genus Polynucleobacter from a shallow eutrophic lake and its tributary was achieved by size-selective filtration with a 0.7-μm pore filter and cultivation on R2A agar medium. Partial 16S rRNA gene analysis showed that over 80% of all the strains were highly similar to the Polynucleobacter cluster. Essential medium components for effective cultivation are pyruvate, yeast extract and peptone, whereas soluble starch and glucose are not necessary. Isolate KF001 (affiliated with Polynucleobacter subcluster D) has a strict requirement for organic acids as carbon sources, and we hypothesize that the Polynucleobacter cluster of bacteria could utilize compounds formed via photochemically dissolved organic matter (DOM) degradation for growth. Because organic acids form from solar radiation of DOM in aquatic environments, carbon sources that are typical products of DOM photochemical degradation were added to the medium. These compounds were readily utilized by KF001 in this study. Finally, we observed the stimulation of strain KF001 activity by photochemical degradation of natural lake water. Our findings suggest a carbon flow of DOM photoproducts to Polynucleobacter in the freshwater microbial loop.     

Latitudinal gradients in degradation of marine dissolved organic carbon

Heterotrophic microbial communities cycle nearly half of net primary productivity in the ocean, and play a particularly important role in transformations of dissolved organic carbon (DOC). The specific means by which these communities mediate the transformations of organic carbon are largely unknown, since the vast majority of marine bacteria have not been isolated in culture, and most measurements of DOC degradation rates have focused on uptake and metabolism of either bulk DOC or of simple model compounds (e.g. specific amino acids or sugars). Genomic investigations provide information about the potential capabilities of organisms and communities but not the extent to which such potential is expressed. We tested directly the capabilities of heterotrophic microbial communities in surface ocean waters at 32 stations spanning latitudes from 76°S to 79°N to hydrolyze a range of high molecular weight organic substrates and thereby initiate organic matter degradation. These data demonstrate the existence of a latitudinal gradient in the range of complex substrates available to heterotrophic microbial communities, paralleling the global gradient in bacterial species richness. As changing climate increasingly affects the marine environment, changes in the spectrum of substrates accessible by microbial communities may lead to shifts in the location and rate at which marine DOC is respired. Since the inventory of DOC in the ocean is comparable in magnitude to the atmospheric CO(2) reservoir, such a change could profoundly affect the global carbon cycle.     

Increasing riverine export of dissolved organic carbon from China

River transport of dissolved organic carbon (DOC) to the ocean is a crucial but poorly quantified regional carbon cycle component. Large uncertainties remaining on the riverine DOC export from China, as well as its trend and drivers of change, have challenged the reconciliation between atmosphere-based and land-based estimates of China's land carbon sink. Here, we harmonized a large database of riverine in-situ measurements and applied a random forest model, to quantify riverine DOC fluxes (F_DOC) and DOC concentrations (C_DOC) in rivers across China. This study proposes the first DOC modeling effort capable of reproducing well the magnitude of riverine C_DOC and F_DOC, as well as its trends, on a monthly scale and with a much wider spatial distribution over China compared to previous studies that mainly focused on annual-scale estimates and large rivers. Results show that over the period 2001–2015, the average C_DOC was 2.25 ± 0.45 mg/L and average F_DOC was 4.04 ± 1.02 Tg/year. Simultaneously, we found a significant increase in F_DOC (+0.044 Tg/year², p = .01), but little change in C_DOC (−0.001 mg/L/year, p > .10). Although the trend in C_DOC is not significant at the country scale, it is significantly increasing in the Yangtze River Basin and Huaihe River Basin (0.005 and 0.013 mg/L/year, p < .05) while significantly decreasing in the Yellow River Basin and Southwest Rivers Basin (−0.043 and −0.014 mg/L/year, p = .01). Changes in hydrology, play a stronger role than direct impacts of anthropogenic activities in determining the spatio-temporal variability of F_DOC and C_DOC across China. However, and in contrast with other basins, the significant increase in C_DOC in the Yangtze River Basin and Huaihe River Basin is attributable to direct anthropogenic activities. Given the dominance of hydrology in driving F_DOC, the increase in F_DOC is likely to continue under the projected increase in river discharge over China resulting from a future wetter climate.     

Spatial uptake of dissolved organic carbon in river beds

The uptake of dissolved organic carbon by three stream bed components; surface stones, underlying gravel and organic floc was measured in three rivers in North Wales, U.K. Overall, surface stones and underlying gravel appeared to be the major sites of uptake but the relative importance of these two components varied both temporally and spatially. Organic floc was found to be relatively unimportant as a site of dissolved organic carbon uptake.     

Seasonal variability of dissolved organic carbon ina Mediterranean stream

The seasonal variability of dissolved organic carbon(DOC) flux in a Mediterranean stream subjected todischarges of wide range of intensities and variabledry period was studied as a function of the hydrologicconditions, and the relationship between surface andsubsurface (hyporheic and groundwater) DOCconcentration. DOC concentration in stream water(2.6 mg l^–1 ±1.5 SD) was higher thangroundwater (1.3 mg l^–1 ± 1.2 SD) and lower thanhyporheic water (3.8 mg l^–1 ±1.7 SD),suggesting that, at baseflow, stream DOC concentrationincreases when groundwater discharges through thehyporheic zone. Storms contributed to 39% of annualwater export and to 52% of the total annual DOCexport (220 kg km^–2). A positive relationship wasobserved between Discharge (Q) and stream DOCconcentration. Discharge explained only 40% of theannual variance in stream DOC, but explained up to93% of the variance within floods. The rate of streamDOC changes with discharge change during storms (dDOC/dQ), ranged between 0 and 0.0045 C mgl^–1 s l^–1, with minimum values during Springand Summer, and maxima values in Fall and Winter.These dynamics suggest that storm inputs ofterrigenous DOC vary between seasons. During floods inthe dormant season, DOC recession curves were alwayssteeper than discharge decline, suggesting shortflushing of DOC from the leaching of fresh detritusstored in the riparian zone.     

Dissolved free amino acids and polyamines are two major dissolved organic nitrogen sources for marine bacterioplankton in the northern slope of the South China Sea

Biogeochemistry - The northern slope water of the South China Sea (SCS) is oligotrophic. The regenerated nitrogen from dissolved organic nitrogen (DON) has been suggested to play a pivotal role in...     

Unimodal response of fish yield to dissolved organic carbon

Here, we demonstrate a contrasting effect of terrestrial coloured dissolved organic material on the secondary production of boreal nutrient poor lakes. Using fish yield from standardised brown trout gill‐net catches as a proxy, we show a unimodal response of lake secondary productivity to dissolved organic carbon (DOC). This suggests a trade‐off between positive and negative effects, where the initial increase may hinge upon several factors such as energy subsidising, screening of UV‐radiation or P and N load being associated with organic carbon. The subsequent decline in production with further increase in DOC is likely associated with light limitations of primary production. We also show that shallow lakes switch from positive to negative effects at higher carbon loads than deeper lakes. These results underpin the major role of organic carbon for structuring productivity of boreal lake ecosystems.     

海洋异养细菌利用溶解有机碳的定量评估

【目的】惰性溶解有机碳(refractory dissolved organic carbon,RDOC)是海洋总有机碳的主体组分,RDOC在深海中可保存数千年,构成了巨大的碳储库,在调节气候变化中有重要作用。但RDOC的定量评估尚未有统一的标准方法。通过测定环境中能被异养细菌利用的溶解有机碳(biodegradable DOC,BDOC)可以反过来评估RDOC的量。本文对BDOC测定中一些关键步骤进行验证,为制定海洋RDOC评估标准奠定基础。【方法】本文评估了3种过滤方式及5种滤膜对DOC测定的影响,并评估了瓶子效应和稀释效应对细菌生长和DOC利用的影响。【结果】研究发现,(1) GF/F滤膜、GF-75滤膜、聚四氟乙烯(PTFE)滤膜(孔径0.2μm)、聚碳酸酯(PC)滤膜(孔径0.2μm)和聚四氟乙烯材质针孔过滤器(HA)(孔径0.2μm) 5种滤膜不会引入DOC污染;抽滤过滤和重力过滤方式过滤效果稳定、无污染,而在线过滤效果不稳定,易污染;(2)不同大小培养体系(30–480 mL;表面积/体积比为:1.64–0.67 cm–1)之间的细菌生长速率和DOC利用量没有显著性差异;(3)培养体系稀释度越高,细菌生长速率越高,对数生长期细菌丰度及DOC利用量越低。【结论】综合考虑,建议BDOC和RDOC测定实验中采用抽滤过滤的方式及不进行稀释的培养体系;常用的滤膜和培养体积对BDOC评估无显著影响。结合研究结果,我们提出了评估海洋RDOC的方法。     

Combining culture-dependent and -independent methodologies for estimation of richness of estuarine bacterioplankton consuming riverine dissolved organic matter

Three different methods for analyzing natural microbial community diversity were combined to maximize an estimate of the richness of bacterioplankton catabolizing riverine dissolved organic matter (RDOM). We also evaluated the ability of culture-dependent quantitative DNA-DNA hybridization, a 16S rRNA gene clone library, and denaturing gradient gel electrophoresis (DGGE) to detect bacterial taxa in the same sample. Forty-two different cultivatable strains were isolated from rich and poor solid media. In addition, 50 unique clones were obtained by cloning of the bacterial 16S rDNA gene amplified by PCR from the community DNA into an Escherichia coli vector. Twenty-three unique bands were sequenced from 12 DGGE profiles, excluding a composite fuzzy band of the Cytophaga-Flavobacterium group. The different methods gave similar distributions of taxa at the genus level and higher. However, the match at the species level among the methods was poor, and only one species was identified by all three methods. Consequently, all three methods identified unique subsets of bacterial species, amounting to a total richness of 97 operational taxonomic units in the experimental system. The confidence in the results was, however, dependent on the current precision of the phylogenetic determination and definition of the species. Bacterial consumers of RDOM in the studied estuary were primarily both cultivatable and uncultivable taxa of the Cytophaga-Flavobacterium group, a concordant result among the methods applied. Culture-independent methods also suggested several not-yet-cultivated beta-proteobacteria to be RDOM consumers.