Recurring seasonal dynamics of microbial communities in stream habitats

Recurring seasonal patterns of microbial distribution and abundance in three third-order temperate streams within the southeast Pennsylvania Piedmont were observed over 4 years. Populations associated with streambed sediments and rocks (epilithon) were identified using terminal restriction length polymorphism (tRFLP) and sequencing of 16S rRNA genes selectively amplified with primers for the bacterial domain. Analyses of the relative magnitudes of tRFLP peak areas by using nonmetric multidimensional scaling resolved clear seasonal trends in epilithic and sediment populations. Oscillations between two dominant groups of epilithic genotypes, explaining 86% of the seasonal variation in the data set, were correlated with temperature and dissolved organic carbon. Sequences affiliated with epilithic phototrophs (cyanobacteria and diatom chloroplasts), a Rhodoferax sp., and a Bacillus species clustered in the summer, whereas sequences most closely related to "Betaproteobacteria" (putative Burkholderia sp.), and a putative cyanobacterium clustered in the fall/spring. The sediment genotypes also clustered into two groups, and these explained 85% of seasonal variation but correlated only with temperature. A summer tRFLP pattern was characterized by prevalence of "Betaproteobacteria," "Gammaproteobacteria," and a Bacillus sp., whereas the winter/spring pattern was characterized by phylotypes most closely related to "Firmicutes," "Gammaproteobacteria," and "Nitrospirae." A close association between these headwater streams and their watersheds was suggested by the recovery of sequences related to microbial populations provisionally attributed to not only freshwaters but also terrestrial habitats.     

Structure and seasonal dynamics of hyporheic zone microbial communities in free-stone rivers of the estern United States

The hyporheic zone of a river is characterized by being nonphotic, exhibiting chemical/redox gradients, and having a heterotrophic food web based on the consumption of organic carbon entrained from surface waters. Hyporheic microbial communities constitute the base of food webs in these environments and are important for maintaining a functioning lotic ecosystem. While microbial communities of rivers dominated by fine-grained sediments are relatively well studied, little is known about the structure and seasonal dynamics of microbial communities inhabiting the predominantly gravel and cobble hyporheic zones of rivers of the western United States. Here, we present the first molecular analysis of hyporheic microbial communities of three different stream types (based on mean base discharge, substratum type, and drainage area), in Montana. Utilizing 16S rDNA phylogeny, DGGE pattern analysis, and qPCR, we have analyzed the prokaryotic communities living on the 1.7 to 2.36 mm grain-size fraction of hyporheic sediments from three separate riffles in each stream. DGGE analysis showed clear seasonal community patterns, indicated similar community composition between different riffles within a stream (95.6–96.6% similarity), and allowed differentiation between communities in different streams. Each river supported a unique complement of species; however, several phylogenetic groups were conserved between all three streams including Pseudomonads and members of the genera Aquabacterium, Rhodoferax, Hyphomicrobium, and Pirellula. Each group showed pronounced seasonal trends in abundance, with peaks during the Fall. The Hyphomicrobium group was numerically dominant throughout the year in all three streams. This work provides a framework for investigating the effects of various environmental factors and anthropogenic effects on microbial communities inhabiting the hyporheic zone.     

The seasonal structure of microbial communities in the Western English Channel

Very few marine microbial communities are well characterized even with the weight of research effort presently devoted to it. Only a small proportion of this effort has been aimed at investigating temporal community structure. Here we present the first report of the application of high‐throughput pyrosequencing to investigate intra‐annual bacterial community structure. Microbial diversity was determined for 12 time points at the surface of the L4 sampling site in the Western English Channel. This was performed over 11 months during 2007. A total of 182 560 sequences from the V6 hyper‐variable region of the small‐subunit ribosomal RNA gene (16S rRNA) were obtained; there were between 11 327 and 17 339 reads per sample. Approximately 7000 genera were identified, with one in every 25 reads being attributed to a new genus; yet this level of sampling far from exhausted the total diversity present at any one time point. The total data set contained 17 673 unique sequences. Only 93 (0.5%) were found at all time points, yet these few lineages comprised 50% of the total reads sequenced. The most abundant phylum was Proteobacteria (50% of all sequenced reads), while the SAR11 clade comprised 21% of the ubiquitous reads and ～12% of the total sequenced reads. In contrast, 78% of all operational taxonomic units were only found at one time point and 67% were only found once, evidence of a large and transient rare assemblage. This time series shows evidence of seasonally structured community diversity. There is also evidence for seasonal succession, primarily reflecting changes among dominant taxa. These changes in structure were significantly correlated to a combination of temperature, phosphate and silicate concentrations.     

Temporal dynamics of microbial communities in microcosms in response to pollutants

Elucidating the mechanisms underlying microbial succession is a major goal of microbial ecology research. Given the increasing human pressure on the environment and natural resources, responses to the repeated introduction of organic and inorganic pollutants are of particular interest. To investigate the temporal dynamics of microbial communities in response to pollutants, we analysed the microbial community structure in batch microcosms that were inoculated with soil bacteria following exposure to individual or combined pollutants (phenanthrene, n‐octadecane, phenanthrene + n‐octadecane and phenanthrene + n‐octadecane + CdCl₂). Subculturing was performed at 10‐day intervals, followed by high‐throughput sequencing of 16S rRNA genes. The dynamics of microbial communities in response to different pollutants alone and in combination displayed similar patterns during enrichment. Specifically, the repression and induction of microbial taxa were dominant, and the fluctuation was not significant. The rate of appearance for new taxa and the temporal turnover within microbial communities were higher than the rates reported in other studies of microbial communities in air, water and soil samples. In addition, conditionally rare taxa that were specific to the treatments exhibited higher betweenness centrality values in the co‐occurrence network, indicating a strong influence on other interactions in the community. These results suggest that the repeated introduction of pollutants could accelerate microbial succession in microcosms, resulting in the rapid re‐equilibration of microbial communities.     

中亚热带4种林分类型土壤微生物生物量碳氮特征及季节变化

以中亚热带常绿阔叶林及由其改造而来的闽楠、毛竹及杉木人工林为研究对象,采用氯仿熏蒸浸提法测定了4种林分类型表层(0～10 cm)和深层(40～60 cm)土壤微生物生物量碳(MBC)和氮(MBN),并分析了其季节变化及与土壤理化性质之间的关系.结果表明: 4种林分类型表层土壤MBC和MBN均以常绿阔叶林最高,其次为闽楠人工林、毛竹人工林和杉木人工林,且前三者显著高于后者;各林分深层土壤MBC和MBN无显著差异.4种林分类型的表层土壤MBC和MBN均显著高于深层土壤,且各土层MBC和MBN均具有明显的季节变化,总体呈现出“夏高冬低”单峰曲线变化模式.相关分析表明,4种林分类型土壤MBC和MBN与土壤有机碳、全氮及土壤温度呈显著正相关关系,与土壤容重呈显著负相关关系.表明常绿阔叶林改造成人工林30多年后,表层土壤MBC和MBN呈下降趋势,其中杉木人工林下降幅度最大(分别下降39.0%和49.8%),而对深层土壤MBC和MBN的影响较小.凋落物数量和质量、土壤有机碳和总氮含量及土壤温度是导致各林分类型土壤微生物生物量碳氮差异和季节变化的主要因素.     

Interannual dynamics of viriobenthos abundance and morphological diversity in Chesapeake Bay sediments

Despite significant implications of viral activity in sediment ecosystems, there are limited data describing how sediment viral assemblages respond to broader ecosystem changes. To document this, the spatial and temporal dynamics of viral and bacterial abundance (BA) and changes in the morphological distribution of viruses were examined within three salinity regions over 2 years. Viral abundances (VA) ranged from 0.2 to 17 × 10(10) viruses mL(-1) sediment while direct bacterial counts ranged from 3.8 to 37 × 10(8) cells mL(-1) sediment. Peaks and valleys in the abundance of extracted viruses and bacteria from surface sediments occurred simultaneously, with lows in February 2004 and highs in April 2003. Across all samples, viral and BA were positively correlated (P < 0.001). Vertical profiles showed a decrease in viral and BA with depth in sediments. Based on transmission electron microscopy results, viruses with diminutive capsids (20-50 nm) and from the Myoviridae and Podoviridae viral family types were dominant within surface sediments. The most morphologically diverse viral assemblages occurred in autumn samples from the sandy, polyhaline station and spring samples from the mesohaline station. Seasonal changes showed an average 72% decrease in VA from spring to winter. These observations support the view that viriobenthos assemblages are responsive to seasonal environmental changes and that viral processes have significant implications for the biogeochemical processes mediated by bacterial communities within Bay sediments.     

Distribution of inorganic species in two Antarctic cryptoendolithic microbial communities

Chemical differences were noted between two Antarctic cryptoendolithic (hidden within rock) microenvironments colonized by different microbial communities. Microenvironments dominated by cyanobacteria (BPC) had a higher pH (pH 7–8) than those dominated by lichen (LTL) (pH 4.5–5.5). In order to understand the interactions between the microbiota and the inorganic environment, the inorganic environment was characterized. Water‐soluble, carbonate‐bound, metal‐oxide, organically bound, and residual inorganic species were sequentially extracted from rock samples by chemical means. Each fraction was then quantified using inductively coupled plasma atomic emission spectrometry. BPC contained much more water‐soluble and carbonate‐bound Ca and Mg than LTL. Metal‐oxide species of Al, Fe, and Mn were more abundant in LTL than BPC. Metal oxides appeared to be mobilized (in the order Mn > Fe > Al) from the LTL lichen zone but remained immobile in BPC sandstone. The distribution of K and P bound to metal oxide reflected the distribution of iron oxide in LTL, an indication of the importance of iron in controlling the availability of nutrients in this ecosystem. Metal oxides in turn were likely controlled or influenced by organic matter associated with the lichen community. Despite overall depletion of Fe, Al, and K in the lichen zone, SEM X‐ray analysis showed that they were enriched in fungal hyphae. Water‐soluble P was present despite the presence of metal oxides, which sequester phosphate. This has biological relevance since P is an essential nutrient.     

Using NCSWAP to simulate seasonal nitrogen dynamics in soil and corn

The objective of this study was to determine if a re-calibrated version of the computer model NCSWAP (version 36) could accurately predict corn growth and soil N dynamics in conventionally tilled (CT) and no-till (NT) corn supplied with legume green manure or ammonium nitrate as N sources. We also attempted to ascertain the reasons for limitations in the model's ability to simulate corn growth and soil N dynamics found by our colleagues in a previous study and to propose potential improvements. The model was calibrated to accurately simulate total available N (N in plant above-ground biomass plus soil nitrate in the 0 to 45 cm profile) for a control and a fertilizer CT treatment in the 1992 growing season. To do so, input values defining the quantities of active soil organic N had to be reduced to 19% of the values proposed by the model developers and a solute transport factor defining the mobile vs. immobile fractions of soil nitrate adjusted from 0.8 to 0.2. The discrepancies between the proposed values and the lower values employed in this study might be due to the uncertainties in quantitatively describing soil N mineralization processes and the way they are handled in the model, as well as the lack of a component simulating macroporous-influenced water flow and solute transport in the model. With the current version, until one knows how to predict what these values are, the model needs to be re-calibrated for each experimental site and condition and thus is of limited value as a general model.With no further adjustment of input values, model validation success was mixed. The model accurately predicted total available N for treatments in the second year of the experiment that had the same N source and tillage as the treatments used for the calibration year but with the different weather and growing conditions. However, total available N was underpredicted where legume green manure was the N source and overpredicted with no-till cultivation. The model was accurate in simulating seasonal corn growth for nearly all the treatments, judged by nonsignificant mean difference (MD) values and highly significant correlation coefficients (r). Prediction of seasonal soil nitrate concentration was less accurate compared to total available N and corn growth variables. Potential improvements in the model's simulation of a no-till system as well as for predicting corn harvest yield and seasonal soil nitrate concentration where N deficiency occurs were discussed.     

Effects of projected future urban land cover on nitrogen and phosphorus runoff to Chesapeake Bay

This paper examined the effects of simulated land cover/land use (LC/LU) change from 2000 to 2030 on nutrient loadings to the Chesapeake Bay. The SPAtially Referenced Regression On Watershed Attributes (SPARROW) model was used with anticipated watershed-wide LC/LU change from a growth forecast model that provides spatially explicit probabilities of conversion to impervious surface. The total nitrogen (TN) and total phosphorus (TP) loadings estimated to enter the Chesapeake Bay were reduced by 20% and 19%, respectively. In general, as development replaced other LC/LUs from 2000 to 2030, TN and TP runoff was significantly reduced by losses of non-point, non-urban source loadings, yields, and land-to-water delivery. The simulation results suggest future changes in landscape composition and configuration at catchment and riparian stream buffer width scales could lower TN and TP runoff to the estuary.     

Effects of urban and non-urban land cover on nitrogen and phosphorus runoff to Chesapeake Bay

The aim of this study was to determine the effects of catchment and riparian stream buffer-wide urban and non-urban land cover/land use (LC/LU) on total nitrogen (TN) and total phosphorus (TP) runoff to the Chesapeake Bay. The effects of the composition and configuration of LC/LU patches were explored in particular. A hybrid-statistical-process model, the SPAtially Referenced Regression On Watershed attributes (SPARROW), was calibrated with year 1997 watershed-wide, average annual TN and TP discharges to Chesapeake Bay. Two variables were predicted: (1) yield per unit watershed area and (2) mass delivered to the upper estuary. The 166,534 km² watershed was divided into 2339 catchments averaging 71 km². LC/LU was described using 16 classes applied to both the catchments and also to riparian stream buffers alone. Seven distinct landscape metrics were evaluated. In all, 167 (TN) and 168 (TP) LC/LU class metric combinations were tested in each model calibration run. Runs were made with LC/LU in six fixed riparian buffer widths (31, 62, 125, 250, 500, and 1000 meters (m)) and entire catchments. The significance of the non-point source type (land cover, manure and fertilizer application, and atmospheric deposition) and factors affecting land-to-water delivery (physiographic province and natural or artificial land surfaces) was assessed. The model with a 31 m riparian stream buffer width accounted for the highest variance of mean annual TN (r² = 0.9366) and TP (r² = 0.7503) yield (mass for a specified time normalized by drainage area). TN and TP loadings (mass for a specified time) entering the Chesapeake Bay were estimated to be 1.449 × 10⁸ and 5.367 × 10⁶ kg/yr, respectively. Five of the 167 TN and three of the 168 TP landscape metrics were shown to be significant (p-value ≤ 0.05) either for non-point sources or land-to-water delivery variables. This is the first demonstration of the significance of riparian LC/LU and landscape metrics on water quality simulation in a watershed as large as the Chesapeake Bay. Land cover metrics can therefore be expected to improve the precision of estimated TN and TP annual loadings to the Chesapeake Bay and may also suggest changes in land management that may be beneficial in control of nutrient runoff to the Chesapeake Bay and similar watersheds elsewhere.     

Genomic structure predicts metabolite dynamics in microbial communities

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施肥对落叶松和水曲柳人工林土壤微生物生物量碳和氮季节变化的影响

2007-2008年,采用氯仿熏蒸浸提法测定了落叶松和水曲柳人工林土壤微生物生物量,研究施N肥对土壤微生物生物量碳、氮,以及细菌、真菌和放线菌数量季节变化的影响.结果表明：落叶松林地土壤微生物生物量碳、氮两年平均值分别比水曲柳林地低13.8%和18.3%,但两种林分土壤微生物生物量碳、氮具有相同的季节变化规律：5月最低,9月最高;表层（0～10 cm）土壤微生物生物量碳、氮及微生物数量均高于亚表层（10～20 cm）土壤.但细菌、真菌和放线菌数量的季节变化格局与生物量不同.施肥降低了两种林分的微生物生物量碳、氮,以及细菌、真菌和放线菌数量,其中,落叶松林地微生物生物量碳和氮分别降低了24%和63%,水曲柳分别降低了51%和68%.说明施N肥限制了土壤微生物生物量,改变了土壤微生物的群落结构.     

不同环境条件下土壤微生物对模拟大气氮沉降的响应

研究了林内及林缘两个生境中,在有苔藓覆盖和无苔藓覆盖条件下,人工加氮对土壤理化性质及土壤微生物群落的影响。结果显示加氮使土壤pH下降,有效态氮和有效态磷的含量上升,但不同生境及有无苔藓植物覆盖在一定程度上影响土壤理化性质及其对加氮的反应。苔藓植物覆盖可以缓解加氮引起的土壤酸化及有效氮含量上升压力,促进有效态磷含量上升。不同生境中,土壤微生物对氮沉降的响应亦不同。低氮使林缘生境土壤微生物的胁迫程度减小,中高氮使其胁迫程度上升,而任何加氮均增加林内生境中土壤微生物的胁迫程度。两个生境中,苔藓植物覆盖均可以缓解过量氮沉降对土壤微生物造成的压力,降低过量氮沉降对土壤微生物的伤害,提高土壤微生物的代谢活性。     

Systematic evaluation of factors controlling Perkinsus marinus transmission dynamics in lower Chesapeake Bay

The transmission of Perkinsus marinus in eastern oysters Crassostrea virginica in relation to water temperature, host oyster mortality, and water-column abundance of anti-P. marinus antibody-labeled cells was systematically examined for 20 mo at a site in the lower York River, Virginia, USA. Uninfected sentinel oysters were naturally exposed to the parasite at 2 wk intervals throughout the course of the study to determine the periodicity and rates of parasite transmission. The timing and magnitude of disease-associated oyster mortalities in a local P. marinus-infected oyster population were estimated by monitoring a captive subset of the local oyster population. Flow cytometric immunodetection methods were employed to estimate the abundance of P. marinus cells in water samples collected 3 times each week. The acquisition of P. marinus infections by na?ve sentinel oysters occurred sporadically at all times of the year; however, the highest incidence of infection occurred during the months of August and September. This window of maximum parasite transmission coincided with the death of infected hosts within the captive local oyster population. Counts of antibody-labeled cells ranged from 10 to 11900 cells l(-1), with the highest abundances in July and August coincident with maximum summer temperatures. A statistically significant relationship between water-column parasite abundance and infection-acquisition rate was not observed; however, highest parasite-transmission rates in both years occurred during periods of elevated water-column abundance of parasite cells. These results support the prevailing model of P. marinus transmission dynamics by which maximum transmission rates are observed during periods of maximum P. marinus-associated host mortality. However, our results also indicate that transmission can occur when host mortality is low or absent, so alternative mortality-independent dissemination mechanisms are likely. The results also suggest that atypically early-summer oyster mortality from Haplosporidium nelsoni infection, at a time when infections of P. marinus are light, has a significant indirect influence on P. marinus transmission dynamics. Elimination of these hosts prior to late-summer P. marinus infection-intensification effectively reduces the overall number of P. marinus cells disseminated.     

Drift dynamics in microbial communities and the effective community size

The structure and diversity of all open microbial communities are shaped by individual births, deaths, speciation and immigration events; the precise timings of these events are unknowable and unpredictable. This randomness is manifest as ecological drift in the population dynamics, the importance of which has been a source of debate for decades. There are theoretical reasons to suppose that drift would be imperceptible in large microbial communities, but this is at odds with circumstantial evidence that effects can be seen even in huge, complex communities. To resolve this dichotomy we need to observe dynamics in simple systems where key parameters, like migration, birth and death rates can be directly measured. We monitored the dynamics in the abundance of two genetically modified strains of Escherichia coli, with tuneable growth characteristics, that were mixed and continually fed into 10 identical chemostats. We demonstrated that the effects of demographic (non-environmental) stochasticity are very apparent in the dynamics. However, they do not conform to the most parsimonious and commonly applied mathematical models, where each stochastic event is independent. For these simple models to reproduce the observed dynamics we need to invoke an ‘effective community size’, which is smaller than the census community size.