Effects of sieving, drying and rewetting upon soil bacterial community structure and respiration rates

Soil microcosm studies often require some form of soil homogenisation, such as sieving, to provide a representative sample. Frequently, soils are also homogenised following drying and are then rewetted, yet little research has been done to understand how these methods impact upon microbial communities. Here we compared the molecular diversity and functional responses of intact cores from a Scottish grassland soil with homogenised samples prepared by drying, sieving and rewetting or freshly sieving wet soils. Results showed that there was no significant difference in total soil CO₂-C efflux between the freshly sieved and intact core treatments, however, respiration was significantly higher in the dried and rewetted microcosms. Molecular fingerprinting (T-RFLP) of bacterial communities at two different time-points showed that both homogenisation methods significantly altered bacterial community structure with the largest differences being observed after drying and rewetting. Assessments of responsive taxa in each treatment showed that intact cores were dominated by Acidobacterial peaks whereas an increased relative abundance of Alphaproteobacterial terminal restriction fragments were apparent in both homogenised treatments. However, the shift in community structure was not as large in the freshly sieved soil. Our findings suggest that if soil homogenisation must be performed, then fresh sieving of wet soil is preferable to drying and rewetting in approximating the bacterial diversity and functioning of intact cores.     

The recovery of benthic foraminifera and bacteria after disturbance: experimental evidence

In experiments with living meiofauna, sediment is often sieved prior to incubation. This is primarily to remove macrofauna and to increase reproducibility among replicates. At the onset of the experiment, the bacteria are severely disturbed. The effects of these disturbances are ill-known but might affect the outcome of the experimental meiofaunal and biogeochemical studies substantially.We compared the disturbance induced by sieving with the disturbance in microcosms from which meiofauna was removed by flushing with argon. Both experimental situations were compared with untreated cores and the field situation. Neither sieving nor flushing induced changes in the composition of the foraminiferal community compared with the natural situation; the four most abundant species found in the field remained dominant during the experiment. Sieving led to a pronounced disturbance in both bacterial as well as foraminiferal abundance patterns. The depth distribution of some species seems to be related to food, although bacteria might play a regulating role as well.     

Assessment of Factors Influencing Direct Enumeration of Viruses within Estuarine Sediments

Accurate enumeration of viruses within environmental samples is critical for investigations of the ecological role of viruses and viral infection within microbial communities. This report evaluates differences in viral and bacterial direct counts between estuarine sediment samples which were either immediately processed onboard ship or frozen at −20°C and later processed. Viral and bacterial abundances were recorded at three stations spanning the length of the Chesapeake Bay in April and June 2003 within three sediment fractions: pore water (PW), whole sediment (WS), and sediment after pore water removal (AP). No significant difference in viral abundance was apparent between extracts from fresh or frozen sediments. In contrast, bacterial abundance was significantly lower in the samples subjected to freezing. Both bacterial and viral abundance showed significant differences between sediment fractions (PW, WS, or AP) regardless of the fresh or frozen status. Although pore water viral abundance has been used in the past as a measurement of viral abundance in sediments, this fraction accounted for only ca. 5% of the total sediment viral abundance across all samples. The effect of refrigerated storage of sediment viral extracts was also examined and showed that, within the first 2 h, viral abundance decreased ca. 30% in formalin-fixed extracts and 66% in unfixed extracts. Finally, the reliability of direct viral enumeration via epifluorescence microscopy was tested by using DNase treatment of WS extractions. These tests indicated that a large fraction (>86%) of the small SYBR gold fluorescing particles are likely viruses.     

Assessment of factors influencing direct enumeration of viruses within estuarine sediments

Accurate enumeration of viruses within environmental samples is critical for investigations of the ecological role of viruses and viral infection within microbial communities. This report evaluates differences in viral and bacterial direct counts between estuarine sediment samples which were either immediately processed onboard ship or frozen at -20 degrees C and later processed. Viral and bacterial abundances were recorded at three stations spanning the length of the Chesapeake Bay in April and June 2003 within three sediment fractions: pore water (PW), whole sediment (WS), and sediment after pore water removal (AP). No significant difference in viral abundance was apparent between extracts from fresh or frozen sediments. In contrast, bacterial abundance was significantly lower in the samples subjected to freezing. Both bacterial and viral abundance showed significant differences between sediment fractions (PW, WS, or AP) regardless of the fresh or frozen status. Although pore water viral abundance has been used in the past as a measurement of viral abundance in sediments, this fraction accounted for only ca. 5% of the total sediment viral abundance across all samples. The effect of refrigerated storage of sediment viral extracts was also examined and showed that, within the first 2 h, viral abundance decreased ca. 30% in formalin-fixed extracts and 66% in unfixed extracts. Finally, the reliability of direct viral enumeration via epifluorescence microscopy was tested by using DNase treatment of WS extractions. These tests indicated that a large fraction (>86%) of the small SYBR gold fluorescing particles are likely viruses.     

The Link between Microbial Diversity and Nitrogen Cycling in Marine Sediments Is Modulated by Macrofaunal Bioturbation

Objectives

The marine benthic nitrogen cycle is affected by both the presence and activity of macrofauna and the diversity of N-cycling microbes. However, integrated research simultaneously investigating macrofauna, microbes and N-cycling is lacking. We investigated spatio-temporal patterns in microbial community composition and diversity, macrofaunal abundance and their sediment reworking activity, and N-cycling in seven subtidal stations in the Southern North Sea.

Spatio-Temporal Patterns of the Microbial Communities

Our results indicated that bacteria (total and β-AOB) showed more spatio-temporal variation than archaea (total and AOA) as sedimentation of organic matter and the subsequent changes in the environment had a stronger impact on their community composition and diversity indices in our study area. However, spatio-temporal patterns of total bacterial and β-AOB communities were different and related to the availability of ammonium for the autotrophic β-AOB. Highest bacterial richness and diversity were observed in June at the timing of the phytoplankton bloom deposition, while richness of β-AOB as well as AOA peaked in September. Total archaeal community showed no temporal variation in diversity indices.

Macrofauna, Microbes and the Benthic N-Cycle

Distance based linear models revealed that, independent from the effect of grain size and the quality and quantity of sediment organic matter, nitrification and N-mineralization were affected by respectively the diversity of metabolically active β-AOB and AOA, and the total bacteria, near the sediment-water interface. Separate models demonstrated a significant and independent effect of macrofaunal activities on community composition and richness of total bacteria, and diversity indices of metabolically active AOA. Diversity of β-AOB was significantly affected by macrofaunal abundance. Our results support the link between microbial biodiversity and ecosystem functioning in marine sediments, and provided broad correlative support for the hypothesis that this relationship is modulated by macrofaunal activity. We hypothesized that the latter effect can be explained by their bioturbating and bio-irrigating activities, increasing the spatial complexity of the biogeochemical environment.     

Free-living nematodes and macrobenthos in a high-latitude glacial fjord

Kongsfjord is an open glacial fjord on the west coast of Svalbard, where the influence of the West Spitzbergen current ameliorates the effects of high latitude (79°N). The fjord is heavily influenced by glacial discharges of meltwater, ice and till, and related environmental gradients in sediments from the glaciers to the open sea include sediment deposition, organic content and disturbance. Other factors, such as the formation and break up of sea ice, also affect benthic communities. In this study spatial patterns in nematode and macrofaunal communities, in samples collected using box-corers and van Veen grabs during a cruise in September 1997, are described, compared and contrasted. Non-parametric multivariate analyses demonstrate that there were clear differences in community structure between stations in both macrofaunal and nematode assemblages. At stations where macrofauna were sampled using both box-cores and grabs there were also significant differences between samples collected by different methods, although there is evidence that these were influenced in part by slight differences in sampling location. Some evidence of disturbance to macrofaunal assemblages in the centre of the fjord is apparent. Macrofaunal community composition varied most closely with a combination of depth and sediment C : N ratio, whereas that of nematodes varied most closely with C : N alone. Proportions of feeding groups of nematodes showed little variation along the fjord. There is no evidence of a specialised nematode assemblage inhabiting the part of the fjord subject to the heaviest deposition of sediment. The taxonomic distinctness of nematodes decreased with increasing distance from the source of disturbance. This is in contrast to studies showing that the taxonomic distinctness of nematodes tends to decrease with increasing anthropogenic stress.     

Weak and Habitat-Dependent Effects of Nutrient Pollution on Macrofaunal Communities of Southeast Australian Estuaries

Among the impacts of coastal settlements to estuaries, nutrient pollution is often singled out as a leading cause of modification to the ecological communities of soft sediments. Through sampling of 48 sites, distributed among 16 estuaries of New South Wales, Australia, we tested the hypotheses that (1) anthropogenic nutrient loads would be a better predictor of macrofaunal communities than estuarine geomorphology or local sediment characteristics; and (2) local environmental context, as determined largely by sediment characteristics, would modify the relationship between nutrient loading and community composition. Contrary to the hypothesis, multivariate multiple regression analyses revealed that sediment grain size was the best predictor of macrofaunal assemblage composition. When samples were stratified according to median grain size, relationships between faunal communities and nitrogen loading and latitude emerged, but only among estuaries with sandier sediments. In these estuaries, capitellid and nereid polychaetes and chironomid larvae were the taxa that showed the strongest correlations with nutrient loading. Overall, this study failed to provide evidence of a differential relationship between diffuse nutrient enrichment and benthic macrofauna across a gradient of 7° of latitude and 4°C temperature. Nevertheless, as human population growth continues to place increasing pressure on southeast Australian estuaries, manipulative field studies examining when and where nutrient loading will lead to significant changes in estuarine community structure are needed.     

Macrofaunal recolonization on intertidal mudflats: effect of sediment organic and sand content

Following concerns over how differences in dredged material properties affects recovery following dredged material deposition on mudflats, a field manipulation experiment was conducted to investigate the effects of increased sediment organic content (from 0.9% to 2.8%) and sand content (from 12.0% to 47.0%) on macrofaunal recolonization and sediment properties on an intertidal mudflat, Crouch Estuary, Essex, UK. The manipulated sediments were placed in 1-m² plots, 10 cm deep, in a randomised block design and macrofauna and sediments sampled after 1 week, 1, 3, 6, and 12 months. The results suggested that while increased sand content had no discernible effect on sediment property changes, increased organic content resulted in marked reductions in redox potential at 1-, 2- and 4-cm sediment depths and increased shear strengths. These sediments exhibited a distinct ‘cracking’ appearance on their surfaces. Similarly, while macrofaunal recovery was only affected by increased sand content in the short-term (1 month), total numbers of individuals, number of species and diversity took longer to recover in sediments with increased organic contents. Recolonization proceeded via a gradual increase in the abundance of those taxa present in ambient sediments rather than via a distinct successional sequence. Recovery was species-specific with two species (Hediste diversicolor (Müller) and Hydrobia ulvae (Pennant)) recovering to ambient levels within the first week of the experiment. Multivariate analyses indicated that the community assemblages of the low-organic content treatments had recovered after 12 months while those of the high-organic content treatments were still significantly different to those of the controls at the end of the experiment. We propose that the relatively rapid recovery and lack of successional sequence generally observed in all sediment types of this study can be explained by the opportunistic nature of the ambient assemblage and by the dispersive nature of the dominant species. Reduced sediments and/or increased shear strengths led to a slow recovery in high-organic content treatments. These results indicate that a careful consideration of the organic content of fine-grained dredged material must be made during the licensing process of beneficial use schemes.     

Microbial Response of a Freshwater Benthic Community to a Simulated Diatom Sedimentation Event: Interactive Effects of Benthic Fauna

Abstract The response of a sediment microbial assemblage to a pulse of diatoms was studied over 36 days by measuring bacterial activity and biomass, ATP concentration, and overall community respiration in laboratory microcosms. Also, the contribution of macrofaunal chironomids to the decomposition of settling diatoms in benthic communities, and the relative importance of benthic meiofauna in community metabolism, were determined. The addition of diatoms resulted in an immediate response by sediment bacteria, with higher bacterial production recorded after only 2 h, and a more than tenfold increase within one day. The rapid response by sediment bacteria was accompanied by relatively high initial concentrations of dissolved organic carbon. In treatments receiving diatoms, higher bacterial production was sustained throughout the experiment. Surprisingly, neither these elevated production estimates, nor the starvation of controls affected bacterial abundance. Mean bacterial cell volume, however, was markedly affected by the addition of diatoms. Combining community respiration measurements and bacterial production estimates showed that growth efficiencies for sediment bacteria ranged from 14.6 to 34.5%. The contribution of ambient meiozoobenthos to carbon metabolism was less than 1%. Carbon budgets showed that 1.3 mg C was cooxidized along with 4.3 mg added diatom C. Sediment reworking by Chironomus larvae initially enhanced bacterial production, but the presence of Chironomus resulted in lower bacterial production estimates after 16 and 36 days. This was interpreted as a result of faster decomposition of diatoms in treatments with chironomids, which was validated by a faster decline of ATP and chlorophyll a in the sediment. Our results indicate that Chironomus larvae compete with sediment bacteria for available organic substrates. Received: 11 June 1996; Accepted: 13 August 1996     

Internal wave-induced redox shifts affect biogeochemistry and microbial activity in sediments: a simulation experiment

Internal waves (seiches) are well-studied physical processes in stratified lakes, but their effects on sediment porewater chemistry and microbiology are still largely unexplored. Due to pycnocline oscillations, sediments are exposed to recurrent changes between epilimnetic and hypolimnetic water. This results in strong differences of environmental conditions, which should be reflected in the responses of redox-sensitive biogeochemical processes at both, the sediment–water interface and deeper sediment layers. We tested in a series of mesocosm experiments the influence of seiche-induced redox changes on porewater chemistry and bacterial activity in the sediments under well controlled conditions. Thereby, we excluded effects of changes in current and temperature regimes. For a period of 10 days, intact sediment cores from oligotrophic Lake Stechlin were incubated under constant (either oxic or anoxic) or alternating redox conditions. Solute concentrations were measured as porewater profiles in the sediment, while microbial activity was determined in the upper 0.5 cm of sediment. Oxic and alternating redox conditions resulted in similar ammonium, phosphate, and methane porewater concentrations, while concentrations of each analyte were considerably higher in anoxic cores. Microbial activity was clearly lower in the anoxic cores than in the oxic and the alternating cores. In conclusion, cores with intermittent anoxic phases of up to 24 hours do not differ in biogeochemistry and microbial activities from static oxic sediments. However, due to various physical processes seiches cause oxygen to penetrate deeper into sediment layers, which affects sediment redox gradients and increase microbial activity in seiche-influenced sediments.     

The effect of wrack composition and diversity on macrofaunal assemblages in intertidal marine sediments

Wrack (dead, washed-up seaweed and seagrass) buried in soft substrata may increase the organic content and alter the physical structure of sediments. These effects may influence the composition and structure of macrofaunal assemblages in the sediment. Such influences can be expected to vary according to the type and amount of wrack as well as the presence of invasive seaweeds in the wrack. In this study, we deliberately buried different amounts of the invasive species Sargassum muticum in isolation or mixed to the native species Ulva sp. and Fucus vesiculosus, in two intertidal sandflats to test some hypotheses about the response of macrofaunal assemblages. We tested whether (1) diversity of detritus (i.e. different mixtures), and (2) the amount of detritus of S. muticum influenced the composition and the relative abundance of macrofaunal assemblages. We also assessed whether the sediment organic carbon and the biomass of benthic microalgae varied depending on the diversity of detritus and the amount of detritus of S. muticum. Finally, we tested if these effects of wrack were consistent across sites. Results indicated that buried wrack affected the composition and structure of macrofaunal assemblages in short-term (i.e. 4 weeks), but there were no differences depending on detritus diversity or the amount of S. muticum. In addition, sediment organic matter and microalgal biomass were not affected by the addition of wrack. They instead varied greatly among small spatial scales (i.e. plots). Wrack composition or abundance of the invasive species S. muticum played thus a small role in shaping the structure of macrofaunal assemblages or the biomass of benthic microalgae in these intertidal sediments, probably because these sediments are frequently affected by various inputs of organic matter and benthic assemblages are already adapted to organically enriched sediments.     

Contrasting dynamics of ciliate communities in sandy and silty sediments of an estuarine intertidal flat

During a 1-year study of the ciliate faunas of a silty and a sandy site on an intertidal flat in the Westerschelde estuary, a total number of 107 taxa were recorded belonging to at least 52 genera and 15 orders. Our results suggest that physical properties of the sediment were more important in regulating ciliate abundance, diversity and community composition than food availability, predation, temperature or oxygen concentration. Ciliate abundance and diversity were positively related to sediment grain size and the ciliate community of silty sediments was found to be a subset of that of sandy sediments. At the sandy site, where the sediment composition was stable, seasonal changes in the ciliate community were related to changes in food availability and/or temperature. At both the sandy and silty sites, a clear vertical gradient in the ciliate community was observed that appeared to be linked to gradients in food availability and oxygen concentration. These vertical gradients in ciliate community composition, however, were less steep than the measured oxygen gradients, probably due to the presence of oxic microniches in the anoxic zone.     

Meiofaunal colonization of azoic estuarine sediment in Louisiana: Mechanisms of dispersal1

Two mechanisms of muddy-bottom meiofaunal dispersal, waterborne suspended transport and holobenthic infaunal immigration, were compared as to their rate and effectiveness in mediating community reestablishment after small-scale defaunation. Colonizing meiofauna were quantitatively sampled in winter and summer from 16 replicates of two azoic sediment chamber designs on 2 and 29 days postplacement. The chambers were ≈ 3750 cm³; one design allowed colonization via suspended movement through an open top, while the other design permitted entry only by infaunal crawling through subsurface open sides. After 48 h, mean harpacticoid copepod and naupliar densities in sediment chambers open to colonization exclusively by meiofauna in suspended transport were not significantly different from background sediment densities. Sediment chambers allowing colonization exclusively via infaunal immigration through the sediment, however, contained copepod and naupliar densities that were significantly less than densities in background sediments and suspension-colonized chambers. In contrast, nematode densities in both suspension- and infaunally colonized chambers were significantly less than in background sediments, but densities were not significantly different between the chamber treatments. Thus for a small-scale defaunation, copepods most rapidly and completely recolonize sediments via suspended transport. Nematode dispersal occurs equally well via suspended or infaunal movement; however nematodes never seemed to utilize the chambers fully because densities did not reach background levels even after 29 days.     

Preservation of Estuarine Sediments for Lipid Analysis of Biomass and Community Structure of Microbiota

Various methods were tested for preserving estuarine sediments in the field before biochemical analysis of the microbiota. Total microbial biomass was determined as lipid phosphate (LP), and the fatty acids of the microbial lipids were used as indicators of community structure. Control samples were sieved to remove macroinvertebrates and plant materials and were extracted immediately in the field. Other samples were preserved both before and after sieving and stored for 5 days before analysis. Freezing resulted in a 50% decline in LP and significant decreases in many fatty acids. Refrigeration resulted in a 19% decrease in LP but no change in the fatty acids. Samples preserved with Formalin before sieving exhibited no significant change in LP but substantial increases in many fatty acids, which were probably derived from the macroinvertebrates. Sieved samples preserved with Formalin showed a 17 to 18% decline in LP but no change in the fatty acids. Ideally, samples should be sieved and extracted immediately in the field. However, short-term refrigeration and longer-term preservation of sieved samples with Formalin may be acceptable compromises.     

Microbial diversity and stratification of South Pacific abyssal marine sediments

Abyssal marine sediments cover a large proportion of the ocean floor, but linkages between their microbial community structure and redox stratification have remained poorly constrained. This study compares the downcore gradients in microbial community composition to porewater oxygen and nitrate concentration profiles in an abyssal marine sediment column in the South Pacific Ocean. Archaeal 16S rRNA clone libraries showed a stratified archaeal community that changed from Marine Group I Archaea in the aerobic and nitrate-reducing upper sediment column towards deeply branching, uncultured crenarchaeotal and euryarchaeotal lineages in nitrate-depleted, anaerobic sediment horizons. Bacterial 16S rRNA clone libraries revealed a similar shift on the phylum and subphylum level within the bacteria, from a complex community of Alpha-, Gamma- and Deltaproteobacteria, Actinobacteria and Gemmatimonadetes in oxic surface sediments towards uncultured Chloroflexi and Planctomycetes in the anaerobic sediment column. The distinct stratification of largely uncultured bacterial and archaeal groups within the oxic and nitrate-reducing marine sediment column provides initial constraints for their microbial habitat preferences.     

Microbial Diversity in Water and Sediment of Lake Chaka, an Athalassohaline Lake in Northwestern China

We employed culture-dependent and -independent techniques to study microbial diversity in Lake Chaka, a unique hypersaline lake (32.5% salinity) in northwest China. It is situated at 3,214 m above sea level in a dry climate. The average water depth is 2 to 3 cm. Halophilic isolates were obtained from the lake water, and halotolerant isolates were obtained from the shallow sediment. The isolates exhibited resistance to UV and gamma radiation. Microbial abundance in the sediments ranged from 10⁸ cells/g at the water-sediment interface to 10⁷ cells/g at a sediment depth of 42 cm. A major change in the bacterial community composition was observed across the interface. In the lake water, clone sequences affiliated with the Bacteroidetes were the most abundant, whereas in the sediments, sequences related to low G+C gram-positive bacteria were predominant. A similar change was also present in the archaeal community. While all archaeal clone sequences in the lake water belonged to the Halobacteriales, the majority of the sequences in the sediments were related to those previously obtained from methanogenic soils and sediments. The observed changes in the microbial community structure across the water-sediment interface were correlated with a decrease in salinity from the lake water (32.5%) to the sediments (approximately 4%). Across the interface, the redox state also changed from oxic to anoxic and may also have contributed to the observed shift in the microbial community.     

The microbial community structure of different permeable sandy sediments characterized by the investigation of bacterial fatty acids and fluorescence in situ hybridization

This study describes the microbial community structure of three sandy sediment stations that differed with respect to median grain size and permeability in the German Bight of the Southern North Sea. The microbial community was investigated using lipid biomarker analyses and fluorescence in situ hybridization. For further characterization we determined the stable carbon isotope composition of the biomarkers. Biomarkers identified belong to different bacterial groups such as members of the Cytophaga-Flavobacterium cluster and sulfate-reducing bacteria (SRB). To support these findings, investigations using different fluorescent in situ hybridization probes were performed, specifically targeting Cytophaga-Flavobacterium, gamma-Proteobacteria and different members of the SRB. Depth profiles of bacterial fatty acid relative abundances revealed elevated subsurface peaks for the fine sediment, whereas at the other sandy sediment stations the concentrations were less variable with depth. Although oxygen penetrates deeper into the coarser and more permeable sediments, the SRB biomarkers are similarly abundant, indicating suboxic to anoxic niches in these environments. We detected SRB in all sediment types as well as in the surface and at greater depth, which suggests that SRB play a more important role in oxygenated marine sediments than previously thought.     

砂质潮间带自由生活海洋线虫对缺氧的响应——微型受控生态系研究

以青岛砂质潮间带自由生活海洋线虫为研究对象,建立微型受控生态系,研究缺氧对海洋线虫群落结构和垂直分布的影响,以及环境复氧后海洋线虫群落的恢复能力。研究结果显示,海洋线虫是耐低氧的小型底栖动物类群,可通过垂直迁移来耐受缺氧造成的不利条件。但是,海洋线虫通过主动迁出而耐受缺氧条件的特性具有种的区别。研究中Pseudosteineria sp1、Rhynchonema sp1等海洋线虫通过向有氧环境的主动迁移耐受缺氧条件;Thalassironus sp1却可通过自身耐受机制抵御缺氧条件,在缺氧生境中仍能保持较高的丰度。此外,研究结果显示,当表层海洋线虫暴露于缺氧环境时,其总丰度显著降低,种类组成发生改变。Pseudosteineria sp1对缺氧环境较为敏感,可暂时性地离开沉积物进入水层;而沉积物溶解氧恢复正常后,该种可以重新回到沉积物中。Daptonema sp1成熟个体及其幼龄个体对缺氧均具有较高的耐受性,是缺氧群落的绝对优势种。D.sp3则表现出对缺氧环境较高的敏感性。环境恢复正常,线虫群落丰度及多样性增加,Neochromadora sp1和Spilophorella sp1等具有机会种的特点,首先表现出丰度和繁殖能力的增加。但是线虫群落种类组成在受测时间内并未能完全恢复,群落结构的恢复需要更长的时间。