Within-trophic group interactions of bacterivorous nematode species and their effects on the bacterial community and nitrogen mineralization

Knowledge of the interactions between organisms within trophic groups is important for an understanding of the role of biodiversity in ecosystem functioning. We hypothesised that interactions between bacterivorous nematodes of different life history strategies would affect nematode population development, bacterial community composition and activity, resulting in increased N mineralization. A microcosm experiment was conducted using three nematode species (Bursilla monhystera, Acrobeloides nanus and Plectus parvus). All the nematode species interacted with each other, but the nature and effects of these interactions depended on the specific species combination. The interaction between B. monhystera and A. nanus was asymmetrically competitive (0,–), whereas that between B. monhystera and P. parvus, and also A. nanus and P. parvus was contramensal (+, –). The interaction that affected microcosm properties the most was the interaction between B. monhystera and P. parvus. This interaction affected the bacterial community composition, increased the bacterial biomass and increased soil N mineralization. B. monhystera and P. parvus have the most different life history strategies, whereas A. nanus has a life history strategy intermediate to those of B. monhystera and P. parvus. We suggest that the difference in life history strategies between species of the same trophic group is of importance for their communal effect on soil ecosystem processes. Our results support the idiosyncrasy hypothesis on the role of biodiversity in ecosystem functioning.     

Responses of algae, bacteria, Daphnia and natural parasite fauna of Daphnia to nutrient enrichment in mesocosms

Understanding responses of parasites to changes in nutrient regimes is necessary for prediction of their role in aquatic ecosystems under global change in nutrient loading. We studied the response of the natural parasite fauna of Daphnia longispina to nutrient enrichment in mesocosms in a small humic lake. We measured the concentrations of inorganic phosphorus and nitrogen in the water, total nutrients in the seston, algal and bacterial biomass, Daphnia population dynamics, Daphnia stoichiometry, Daphnia stable isotope values and the presence and abundance of parasites in treated mesocosms as compared to three control ones. Incorporation of the nutrient enrichment in the food web was seen as increased nutrient concentrations in the epilimnion and as a decrease in carbon:nutrient ratios and δ¹⁵N values in Daphnia. Nutrient enrichment did not significantly influence algal, bacterial or Daphnia biomass. One of the four parasite species observed, unidentified small gut parasite, had a higher prevalence (percentage of Daphnia infected) in treated mesocosms, but its intensity (number of parasites per infected host) remained the same among treatments. Our results suggest that the effect of nutrient enrichment on host–parasite dynamics is dependent on complex interactions within food webs and on the epidemiological traits of parasites.     

Long-term nutrient enrichment elicits a weak density response by saltmarsh meiofauna

The effect of chronic nutrient enrichment on benthic meiofauna was examined in a whole-ecosystem experiment conducted in salt marshes in the Plum Island watershed of northeastern Massachusetts, USA. We compared abundances of total meiofauna, nematodes, copepods, ostracods, and annelids including Manayunkia aestuarina, in fertilized (where N and P was increased 15× in incoming tidal water throughout each growing season for 6 years) and reference marsh creeks to test for bottom-up responses. Although some responses to nutrient enrichment were evident, results did not match our expectations of strong increases in abundance. Variation in abundance between nutrient-enriched and reference creeks was detected in all three subhabitats but responses were inconsistent and variable over time, suggesting that natural variability was greater than variation induced by fertilization. Our results showed an overall weak negative correlation between meiofauna abundance and benthic microalgae (BMA) biomass partly because the BMA response to nutrient enrichment was relatively small and perhaps limited by grazing macrofauna and nekton. Our results suggest a better mechanistic understanding of the relationship between BMA and meiofaunal abundance is needed to fully understand how nutrient enrichment affects meiofauna.     

The Pattern of Change in the Abundances of Specific Bacterioplankton Groups Is Consistent across Different Nutrient-Enriched Habitats in Crete

A common source of disturbance for coastal aquatic habitats is nutrient enrichment through anthropogenic activities. Although the water column bacterioplankton communities in these environments have been characterized in some cases, changes in α-diversity and/or the abundances of specific taxonomic groups across enriched habitats remain unclear. Here, we investigated the bacterial community changes at three different nutrient-enriched and adjacent undisturbed habitats along the north coast of Crete, Greece: a fish farm, a closed bay within a town with low water renewal rates, and a city port where the level of nutrient enrichment and the trophic status of the habitat were different. Even though changes in α-diversity were different at each site, we observed across the sites a common change pattern accounting for most of the community variation for five of the most abundant bacterial groups: a decrease in the abundance of the Pelagibacteraceae and SAR86 and an increase in the abundance of the Alteromonadaceae, Rhodobacteraceae, and Cryomorphaceae in the impacted sites. The abundances of the groups that increased and decreased in the impacted sites were significantly correlated (positively and negatively, respectively) with the total heterotrophic bacterial counts and the concentrations of dissolved organic carbon and/or dissolved nitrogen and chlorophyll α, indicating that the common change pattern was associated with nutrient enrichment. Our results provide an in situ indication concerning the association of specific bacterioplankton groups with nutrient enrichment. These groups could potentially be used as indicators for nutrient enrichment if the pattern is confirmed over a broader spatial and temporal scale by future studies.     

Distributions of Competing Container Mosquitoes Depend on Detritus Types, Nutrient Ratios, and Food Availability

Coexistence of competitors may result if resources are sufficiently abundant to render competition unimportant, or if species differ in resource requirements. Detritus type has been shown to affect interspecific competitive outcomes between Aedes albopictus (Skuse) and Aedes aegypti (L.) larvae under controlled conditions. We assessed the relationships among spatial distributions of detritus types, nutrients, and aquatic larvae of these species in nature. We collected mosquitoes, water, and detritus from artificial containers across 24 Florida cemeteries that varied in relative abundances of Ae. aegypti and Ae. albopictus.We measured nutrient content of fine particulate organic matter in water samples as total N, P, and C and ratios of these nutrients. We quantified food availability via a bioassay, raising individual Aedes larvae in the laboratory in standard volumes of field-collected, particulate-containing water from each cemetery. Quantities of detritus types collected in standard containers were significant predictors of nutrients and nutrient ratios. Nutrient abundances were significant predictors of relative abundance of Ae. aegypti, and of larval survival and development by both species in the bioassay. Survival and development of larvae reared in particulate-containing water from sites decreased with decreasing relative abundance of Ae. aegypti. These data suggest that N, P, and C availabilities are determined by detritus inputs to containers and that these nutrients in turn determine the feeding environment encountered by larvae, the intensity of interspecific competition among larvae, and subsequent relative abundances of species at sites. Detritus inputs, nutrients, and food availability thus seem to contribute to distributions of Ae. aegypti and Ae. albopictus in cemetery containers throughout Florida.     

Temporal fermentation and microbial community dynamics in rumens of sheep grazing a ryegrass-based pasture offered either in the morning or in the afternoon

Eight ruminally-fistulated wethers were used to examine the temporal effects of afternoon (PM; 1600h) v. morning (AM; 0800 h) allocation of fresh spring herbage from a perennial ryegrass (Lolium perenne L.)-based pasture on fermentation and microbial community dynamics. Herbage chemical composition was minimally affected by time of allocation, but daily mean ammonia concentrations were greater for the PM group. The 24-h pattern of ruminal fermentation (i.e. time of sampling relative to time of allocation), however, varied considerably for all fermentation variables (P⩽0.001). Most notably amongst ruminal fermentation characteristics, ammonia concentrations showed a substantial temporal variation; concentrations of ammonia were 1.7-, 2.0- and 2.2-fold greater in rumens of PM wethers at 4, 6 and 8h after allocation, respectively, compared with AM wethers. The relative abundances of archaeal and ciliate protozoal taxa were similar across allocation groups. In contrast, the relative abundances of members of the rumen bacterial community, like Prevotella 1 (P=0.04), Bacteroidales RF16 group (P=0.005) and Fibrobacter spp. (P=0.008) were greater for the AM group, whereas the relative abundance of Kandleria spp. was greater (P=0.04) for the PM group. Of these taxa, only Prevotella 1 (P=0.04) and Kandleria (P<0.001) showed a significant interaction between time of allocation and time of sampling relative to feed allocation. Relative abundances of Prevotella 1 were greater at 2h (P=0.05), 4h (P=0.003) and 6h (P=0.01) after AM allocation of new herbage, whereas relative abundances of Kandleria were greater at 2h (P=0.003) and 4h (P<0.001) after PM allocation. The early post-allocation rise in ammonia concentrations in PM rumens occurred simultaneously with sharp increases in the relative abundance of Kandleria spp. and with a decline in the relative abundance of Prevotella. All measures of fermentation and most microbial community composition data showed highly dynamic changes in concentrations and genus abundances, respectively, with substantial temporal changes occurring within the first 8h of allocating a new strip of herbage. The dynamic changes in the relative abundances of certain bacterial groups, in synchrony with a substantial diurnal variation in ammonia concentrations, has potential effects on the efficiency by which N is utilised by the grazing ruminant.     

The meiofauna of artificial water-filled tree holes: colonization and bottom-up effects

The meiofaunal community of artificial water-filled tree holes was determined, and the bottom-up effects of different amounts of leaf litter on abundance and diversity were estimated. We assume a positive impact of leaf litter on meiofaunal abundances, species diversity, and trophic links. Plastic cups with different amounts of leaf litter were placed in a beech forest (Teutoburg Forest, Bielefeld, Germany) for 24 weeks. As early as 1 week later, the artificial tree holes were colonized by bdelloid rotifers, tardigrades, and nematodes. Rotifers were dominant throughout the experiment, followed by nematodes and tardigrades. The 29 nematode species that were identified included bacterial and hyphal feeders, with common species such as Plectus cirratus/accuminatus and Aphelenchoides parietinus predominating. Impacts of water volume (up to complete desiccation), pH, and O₂ on the meiofaunal community were not detected, whereas the addition of leaf litter resulted in bottom-up effects. Nematode abundance, especially that of bacterial feeders, and species number increased with increasing leaf input. The predatory nematode Prionchulus muscorum was found only in treatments containing high leaf content. Rotifer abundances were partly negatively affected by the amount of added leaves and, like tardigrades, showed a reversal in their correlation at higher leaf inputs. Our study revealed the fast colonization of small water bodies by meiofaunal organisms and the importance of passively distribution. Furthermore, the results provide a comparison with the meiofaunal community in lakes and soil.     

Comparative and experimental approaches to top-down and bottom-up regulation of bacteria

The regulation of bacterial community biomass and productivity by resources and predators is a central concern in the study of microbial food webs. Resource or bottom-up regulation refers to the limitation of bacteria by carbon and nutrients derived from allocthonous inputs, primary production, and heterotrophic production. Predatory or top-down regulation refers to the limitation of bacteria below levels supportable by resources alone. Large scale comparative studies demonstrate strong correlations between bacterial productivity and biomass, suggesting significant resource regulation. Comparisons of the abundances of heterotrophic flagellates and bacteria, however, imply that in some cases there may be top-down regulation of bacteria in eutrophic environments. Experimental studies in lakes support the importance of resource regulation and reveal little top-down control from protozoans. Increases in bacterial abundance and production with nutrient enrichment were limited in enclosure experiments with high abundances of the cladoceran, Daphnia. Regulation of bacteria by Daphnia may occur in many lakes seasonally and prevail in some lakes throughout the year where these animals sustain dense populations. In most situations, however, bacteria appear to be limited primarily by resources.     

Clockwise and counterclockwise hysteresis characterize state changes in the same aquatic ecosystem

Incremental increases in a driver variable, such as nutrients or detritus, can trigger abrupt shifts in aquatic ecosystems that may exhibit hysteretic dynamics and a slow return to the initial state. A model system for understanding these dynamics is the microbial assemblage that inhabits the cup‐shaped leaves of the pitcher plant Sarracenia purpurea. With enrichment of organic matter, this system flips within three days from an oxygen‐rich state to an oxygen‐poor state. In a replicated greenhouse experiment, we enriched pitcher‐plant leaves at different rates with bovine serum albumin (BSA), a molecular substitute for detritus. Changes in dissolved oxygen (DO) and undigested BSA concentration were monitored during enrichment and recovery phases. With increasing enrichment rates, the dynamics ranged from clockwise hysteresis (low), to environmental tracking (medium), to novel counter‐clockwise hysteresis (high). These experiments demonstrate that detrital enrichment rate can modulate a diversity of hysteretic responses within a single aquatic ecosystem, and suggest different management strategies may be needed to mitigate the effects of high vs. low rates of detrital enrichment.     

The effect of bacterivorous nematodes on detritus incorporation by macrofaunal detritivores: A study using stable isotope and fatty acid analyses

Several studies have investigated the effect of nematodes on microbial degradation of macrophyte detritus, but little is known about the potential effect of bacterivorous nematodes on productivity of macrofaunal detritivores. We investigated the influence of the bacterivorous nematode Rhabditis (Pellioditis) mediterranea on the incorporation rate of isotopically-labelled macroalgal detritus by the amphipod Paramoera chevreuxi in a laboratory microcosm. The fatty acid composition of amphipods, nematodes, and macroalgal detritus was characterized to help determine the pathway of detritus incorporation by amphipods. The potential importance of R. mediterranea as a source of highly unsaturated fatty acids (HUFAs) to higher trophic levels was also investigated.We found no clear evidence for an effect of nematodes on the incorporation rate of fresh macroalgal detritus by amphipods, although there was some indication that the type of detritus (i.e. the green Chaetomorpha sp. vs the red Polysiphonia sp.) is important in determining the nature and extent of the relationship between nematodes and macrofaunal detritivores. Fatty acid data indicated that nematodes did not contribute significantly to the diet of amphipods when detritus was present, and there was no evidence that nematodes affected the pathway of detritus incorporation by amphipods. Amphipods incorporated Chaetomorpha sp. detritus about 10 times faster than Polysiphonia sp. detritus despite the higher C/N ratio and lower HUFA content of the former. This suggests that other factors, such as the presence of grazer deterrent compounds, are important in determining the palatability of macroalgal detritus. Amphipods fed exclusively on nematodes retained high HUFA levels but suffered high mortality. The burrowing behaviour of nematodes is suggested as the most likely factor limiting their availability to predators.Results suggest a limited interaction between amphipods and bacterivorous nematodes in detrital food webs. Further experiments are needed to test the wider applicability of these findings to different nematode and macrofaunal taxa, and for different types of detritus.     

氮磷添加对草甸草原土壤氮磷转化功能基因丰度的影响

氮添加是提高退化草地生产力的主要养分管理措施,而过量的氮输入会导致土壤酸化、增加硝酸盐淋溶损失和温室气体排放。旨在明确草原割草利用下土壤氮、磷转化功能基因丰度对氮磷添加的响应规律,为定向调控打草场土壤氮、磷转化过程,提高养分利用效率,减少温室气体N₂O排放提供科学依据。2018—2020年在呼伦贝尔草甸草原打草场设置了5个施氮水平(0、1.55、4.65、13.95、27.9 g N m^-2 a^-1)和3个磷水平(0、5.24、10.48 g P m^-2 a^-1),裂区试验设计,在植物不同生长时期测定土壤氨氧化(amoA-AOA和amoA-AOB)、反硝化(narG、nirK、nirS和nosZ)和磷转化(phoD)基因丰度。结果表明,土壤氮转化基因丰度受到氮、磷添加的调控,而氮、磷添加对土壤磷转化功能基因丰度无显著影响(P>0.05)。氮添加可提高amoA-AOB基因丰度,增加氨氧化细菌调控土壤总硝化速率的相对重要性,因此能增加硝酸盐淋溶损失潜势。高氮处理下添加磷可降低...     

The effect of macrofauna,meiofauna and microfauna on the degradation of Spartina maritima detritus from a salt marsh area

Decomposition of salt marsh plants results from physical, chemical and biological processes including abiotic and biotic fragmentation, microbial decay and chemical transformation. According to literature data, only a few species have the ability to feed directly on living plant material, so fungi and bacteria seem to be the principal competitors for the organic substrates. Nevertheless, by consuming bacteria, protists and fungi associated to the detritus, macrofauna and meiofauna recycle the incorporated nutrients. Moreover, this nutrient regeneration may be seen as an effective factor in maintaining and stimulating bacterial production. In fact, it is well known that many detritus feeding species have very low assimilation efficiencies. The objective of the present study was to compare the nutrient mass balance of carbon; nitrogen and phosphorus in Spartina maritima covered areas and bare bottom sediment, with and without contribution of macrofauna, meiofauna and microbial populations. Nutrients mass balance was studied taking into account the initial and final nutrient concentrations in the sediment, water and plant material. Faunal activity was measured as a function of remineralised carbon, nitrogen and phosphorus. The experimental set-up included sixteen sub-experiments, which varied with respect to type of fauna, plant biomass and oxic status. Each sub-experiment was performed in small glass containers (3 L) containing about 900 g wwt sediment and 2.5 L estuarine water. Plant material, cut from intact plants, sediment cores and estuarine water were brought from the southern arm of the Mondego estuary (Portugal). The results showed that although the bacterial activity was responsible for the Spartina maritima degradation, the presence of meiofauna and macrofauna significantly enhanced the process. Moreover, the presence of Spartina maritima positively affected the mineralisation of the sediment carbon and nitrogen, especially when the three faunal components were present, and denitrification rates were highest in the presence of the macrofauna and meiofauna. The present study suggests that macrofauna and meiofauna have an important role on the ecosystem nutrient flux and that fauna might function as a sink for excess nutrients, that otherwise could be exported to the coastal waters.     

Quality or quantity: is nutrient transfer driven more by symbiont identity and productivity than by symbiont abundance?

By forming symbiotic interactions with microbes, many animals and plants gain access to the products of novel metabolic pathways. We investigated the transfer of symbiont-derived carbon and nitrogen to the sponges Aplysina cauliformis, Aplysina fulva, Chondrilla caribensis, Neopetrosia subtriangularis and Xestospongia bocatorensis, all of which host abundant microbial populations, and Niphates erecta, which hosts a sparse symbiont community. We incubated sponges in light and dark bottles containing seawater spiked with ¹³C- and ¹⁵N-enriched inorganic compounds and then measured ¹³C and ¹⁵N enrichment in the microbial (nutrient assimilation) and sponge (nutrient transfer) fractions. Surprisingly, although most sponges hosting abundant microbial communities were more enriched in ¹³C than N. erecta, only N. subtriangularis was more enriched in ¹⁵N than N. erecta. Although photosymbiont abundance varied substantially across species, ¹³C and ¹⁵N enrichment was not significantly correlated with photosymbiont abundance. Enrichment was significantly correlated with the ratio of gross productivity to respiration (P:R), which varied across host species and symbiont phylotype. Because irradiance impacts P:R ratios, we also incubated A. cauliformis in ¹³C-enriched seawater under different irradiances to determine whether symbiont carbon fixation and transfer are dependent on irradiance. Carbon fixation and transfer to the sponge host occurred in all treatments, but was greatest at higher irradiances and was significantly correlated with P:R ratios. Taken together, these results demonstrate that nutrient transfer from microbial symbionts to host sponges is influenced more by host–symbiont identities and P:R ratios than by symbiont abundance.     

Transformation of detritus by a European native and two invasive alien freshwater decapods

Invasive alien species have the potential to alter biodiversity and ecosystem processes. In freshwaters, detritus decomposition is a major ecosystem service but it remains uncertain whether invasive alien decapods process detritus differently to natives. This study examined leaf litter processing, and cascading effects on biofilms, by the European native white clawed crayfish (Austropotamobius pallipes) compared to two invasive alien decapod species: the American signal crayfish (Pacifastacus leniusculus) and the Chinese mitten crab (Eriocheir sinensis). Invasive alien decapods were responsible for higher leaf litter decomposition than the native. In comparison with native crayfish, invasive alien crab and crayfish showed higher rates of litter consumption, increased production of smaller leaf fragments, fine particulate organic matter (FPOM) and dissolved organic carbon. Nutrients (ammonia and soluble reactive phosphorous) derived from excretion (measured separately in the absence of biofilms) varied among decapod species, being lower for P. leniusculus. However, nutrient concentrations did not vary among species in the detritivory experiments with biofilm, implying nutrients were utilised for biofilm production and respiration as no differences in biomass were evident among decapod treatments. These results show invasive alien decapods have the potential to increase the magnitude of detrital processing to FPOM in rivers, but indirect impacts on primary producers due to nutrient release are uncertain based on this experimental context.     

Protozoa,Nematoda and Lumbricidae in the rhizosphere of Hordelymus europeaus (Poaceae): faunal interactions,response of microorganisms and effects on plant growth

Interactions among protozoa (mixed cultures of ciliates, flagellates and naked amoebae), bacteria-feeding nematodes (Pellioditis pellio Schneider) and the endogeic earthworm species Aporrectodea caliginosa (Savigny) were investigated in experimental chambers with soil from a beechwood (Fagus sylvatica L.) on limestone. Experimental chambers were planted with the grass Hordelymus europeaus L. (Poaceae) and three compartments separated by 45-m mesh were established: rhizosphere, intermediate and non-rhizosphere. The experiment lasted for 16 weeks and the following parameters were measured at the end of the experiment: shoot and root mass of H. europaeus, carbon and nitrogen content in shoots and roots, density of ciliates, amoebae, flagellates and nematodes, microbial biomass (SIR), basal respiration, streptomycin sensitive respiration, ammonium and nitrate contents, phosphate content of soil compartments. In addition, leaching of nutrients (nitrogen and phosphorus) and leachate pH were measured at regular intervals in leachate obtained from suction cups in the experimental chambers. Protozoa stimulated the recovery of nitrifying bacteria following defaunation (by chloroform fumigation) and increased nitrogen losses as nitrate in leachate. In contrast, protozoa and nematodes reduced leaching of phosphate, an effect ascribed to stimulation of microbial growth early in the experiment. Earthworms strongly increased the amount of extractable mineral nitrogen whereas it was strongly reduced by protozoa and nematodes. Both protozoa and nematodes reduced the stimulatory effect of earthworms on nitrogen mineralization. Microbial biomass, basal respiration, and numbers of protozoa and nematodes increased in the vicinity of the root. Protozoa generally caused a decrease in microbial biomass whereas nematodes and earthworms reduced microbial biomass only in the absence of protozoa. None of the animals studied significantly affected basal respiration, but specific respiration of microorganisms (O₂ consumption per unit biomass) was generally higher in animal treatments. The stimulatory effect of nematodes and earthworms, however, occurred only in the absence of protozoa. The sensitivity of respiration to streptomycin suggested that protozoa selectively grazed on bacterial biomass but the bacterial/fungal ratio appeared to be unaffected by grazing of P. pellio. Earthworms reduced root biomass of H. europaeus, although shoot biomass remained unaffected, and concentrations of nitrogen in shoots and particularly in roots were strongly increased by earthworms. Both nematodes and protozoa increased plant biomass, particularly that of roots. This increase in plant biomass was accompanied by a marked decrease in nitrogen concentrations in roots and to a lesser extent in shoots. Generally, the effects of protozoa on plant growth considerably exceeded those of nematodes. It is concluded that nematodes and protozoa stimulated plant growth by non-nutritional effects, whereas the effects of earthworms were caused by an increase in nutrient supply to H. europaeus.     

Increasing Levels of Physical Disturbance Affect Soil Nematode Community Composition in a Previously Undisturbed Ecosystem

Soil is essential for the sustenance of life. Diverse soil organisms support several biological processes such as organic matter decomposition, mineralization, nutrient cycling, and controlling pests and diseases. Among multicellular soil organisms, nematodes are ubiquitous, functionally diverse, and abundant. Notably, agricultural practices have diverse impacts on plants, soils, and soil organisms. Tillage affects nematodes directly by altering pore size and disrupting the continuity of water films and indirectly by affecting the lower trophic groups such as bacteria and fungi. The primary goal of this study was to examine the effect of increasing levels of physical disturbance on nematode communities in an undisturbed forest ecosystem. The experiment included four treatments: control with no disturbance, surface litter removed with no litter and no vegetation, tilling the soil with a rototiller every 2 mon, and every 2 wk. Tillage significantly reduced the overall abundance and overall richness of nematode communities over time. Among nematode trophic groups, tillage significantly reduced the abundance and richness of bacterial feeders, predators, and omnivores over time. The abundance and richness of c-p 2, c-p 4, and c-p 5 class nematodes were significantly decreased by tillage. Unlike tillage, minimal disturbance such as removal of surface litter resulted in a significant decrease in the abundance of only three genera: Acrobeles, Aporcelaimellus, and Boleodorus. Nonmetric multidimensional scaling analysis revealed that nematodes of higher c-p classes such as Dorylaimida, Aporcelaimellus, Alaimus, Clarkus, and Tripyla were sensitive to physical disturbances. Bacterial feeders belonging to the c-p 2 class such as Tylocephalus, Acrobeles, Ceratoplectus, Plectus, and Pseudacrobeles were significantly reduced by tillage. Moreover, tillage significantly reduced the functional metabolic footprint of nematodes, which indicates decreased metabolic activity, reduced C inflow, and poorly structured soil food webs. Previous studies conducted in agricultural ecosystems determined that Clarkus, Filenchus, and Plectus were tolerant to tillage; however, they were found sensitive to tillage in our study. Overall, our study suggests that increasing levels of physical disturbance are detrimental to nematode community abundance and diversity that could affect soil ecosystem stability and sustainability.     

Diverse,rare microbial taxa responded to the Deepwater Horizon deep-sea hydrocarbon plume

The Deepwater Horizon (DWH) oil well blowout generated an enormous plume of dispersed hydrocarbons that substantially altered the Gulf of Mexico''s deep-sea microbial community. A significant enrichment of distinct microbial populations was observed, yet, little is known about the abundance and richness of specific microbial ecotypes involved in gas, oil and dispersant biodegradation in the wake of oil spills. Here, we document a previously unrecognized diversity of closely related taxa affiliating with Cycloclasticus, Colwellia and Oceanospirillaceae and describe their spatio-temporal distribution in the Gulf''s deepwater, in close proximity to the discharge site and at increasing distance from it, before, during and after the discharge. A highly sensitive, computational method (oligotyping) applied to a data set generated from 454-tag pyrosequencing of bacterial 16S ribosomal RNA gene V4–V6 regions, enabled the detection of population dynamics at the sub-operational taxonomic unit level (0.2% sequence similarity). The biogeochemical signature of the deep-sea samples was assessed via total cell counts, concentrations of short-chain alkanes (C₁–C₅), nutrients, (colored) dissolved organic and inorganic carbon, as well as methane oxidation rates. Statistical analysis elucidated environmental factors that shaped ecologically relevant dynamics of oligotypes, which likely represent distinct ecotypes. Major hydrocarbon degraders, adapted to the slow-diffusive natural hydrocarbon seepage in the Gulf of Mexico, appeared unable to cope with the conditions encountered during the DWH spill or were outcompeted. In contrast, diverse, rare taxa increased rapidly in abundance, underscoring the importance of specialized sub-populations and potential ecotypes during massive deep-sea oil discharges and perhaps other large-scale perturbations.     

Catabolic diversity of periphyton and detritus microbial communities in a subtropical wetland

The catabolic diversity of wetland microbial communities may be a sensitive indicator of nutrient loading or changes in environmental conditions. The objectives of this study were to assess the response of periphyton and microbial communities in water conservation area-2a (WCA-2a) of the Everglades to additions of C-substrates and inorganic nutrients. Carbon dioxide and CH₄ production rates were measured using 14 days incubation for periphyton, which typifies oligotrophic areas, and detritus, which is prevalent at P-impacted areas of WCA-2a. The wetland was characterized by decreasing P levels from peripheral to interior, oligotrophic areas. Microbial biomass and N mineralization rates were higher for oligotrophic periphyton than detritus. Methane production rates were also higher for unamended periphyton (80 mg CH₄-C kg⁻¹ d⁻¹) than detritus (22 mg CH₄-C kg⁻¹ d⁻¹), even though the organic matter content was higher for detritus (80%) than periphyton (69%). Carbon dioxide production for unamended periphyton (222 mg CO₂-C kg⁻¹ d⁻¹) was significantly greater than unamended detritus (84 mg CO₂-C kg⁻¹ d⁻¹). The response of the heterotrophic microbial community to added C-substrates was related to the nutrient status of the wetland, as substrate-induced respiration (SIR) was higher for detritus than periphyton. Amides and polysaccharides stimulated SIR more than other C-substrates, and methanogenesis was greater contributor to SIR for periphyton than detritus. Inorganic P addition stimulated CO₂ and CH₄ production for periphyton but not detritus, indicating a P limitation in the interior areas of WCA-2a. Continued nutrient loading into oligotrophic areas of WCA-2a or enhanced internal nutrient cycling may stimulate organic matter decomposition and further contribute to undesirable changes to the Everglades ecosystem caused by nutrient enrichment.     

Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem

Marine microbial communities experience daily fluctuations in light and temperature that can have important ramifications for carbon and nutrient cycling. Elucidation of such short time scale community-wide dynamics is hindered by system complexity. Hypersaline aquatic environments have lower species richness than marine environments and can be well-defined spatially, hence they provide a model system for diel cycle analysis. We conducted a 3-day time series experiment in a well-defined pool in hypersaline Lake Tyrrell, Australia. Microbial communities were tracked by combining cultivation-independent lipidomic, metagenomic and microscopy methods. The ratio of total bacterial to archaeal core lipids in the planktonic community increased by up to 58% during daylight hours and decreased by up to 32% overnight. However, total organism abundances remained relatively consistent over 3 days. Metagenomic analysis of the planktonic community composition, resolved at the genome level, showed dominance by Haloquadratum species and six uncultured members of the Halobacteriaceae. The post 0.8 μm filtrate contained six different nanohaloarchaeal types, three of which have not been identified previously, and cryo-transmission electron microscopy imaging confirmed the presence of small cells. Notably, these nano-sized archaea showed a strong diel cycle, with a pronounced increase in relative abundance over the night periods. We detected no eukaryotic algae or other photosynthetic primary producers, suggesting that carbon resources may derive from patchily distributed microbial mats at the sediment-water interface or from surrounding land. Results show the operation of a strong community-level diel cycle, probably driven by interconnected temperature, light abundance, dissolved oxygen concentration and nutrient flux effects.     

Microbial signatures of protected and impacted Northern Caribbean reefs: changes from Cuba to the Florida Keys

There are a few baseline reef-systems available for understanding the microbiology of healthy coral reefs and their surrounding seawater. Here, we examined the seawater microbial ecology of 25 Northern Caribbean reefs varying in human impact and protection in Cuba and the Florida Keys, USA, by measuring nutrient concentrations, microbial abundances, and respiration rates as well as sequencing bacterial and archaeal amplicons and community functional genes. Overall, seawater microbial composition and biogeochemistry were influenced by reef location and hydrogeography. Seawater from the highly protected ‘crown jewel’ offshore reefs in Jardines de la Reina, Cuba had low concentrations of nutrients and organic carbon, abundant Prochlorococcus, and high microbial community alpha diversity. Seawater from the less protected system of Los Canarreos, Cuba had elevated microbial community beta-diversity whereas waters from the most impacted nearshore reefs in the Florida Keys contained high organic carbon and nitrogen concentrations and potential microbial functions characteristic of microbialized reefs. Each reef system had distinct microbial signatures and within this context, we propose that the protection and offshore nature of Jardines de la Reina may preserve the oligotrophic paradigm and the metabolic dependence of the community on primary production by picocyanobacteria.