Contrasted ecological niches shape fungal and prokaryotic community structure in mangroves sediments

Mangroves are forest ecosystems located at the interface between land and sea where sediments presented a variety of contrasted environmental conditions (i.e. oxic/anoxic, non-sulfidic/sulfidic, organic matter content) providing an ideal ecosystem to study microbial communities with niche differentiation and distinct community structures. In this work, prokaryotic and fungal compositions were investigated during both wet and dry seasons in New Caledonian mangrove sediments, from the surface to deeper horizons under the two most common tree species in this region (Avicennia marina and Rhizophora stylosa), using high-throughput sequencing. Our results showed that Bacteria and Archaea communities were mainly shaped by sediment depth while the fungal community was almost evenly distributed according to sediment depth, vegetation cover and season. A detailed analysis of prokaryotic and fungal phyla showed a dominance of Ascomycota over Basidiomycota whatever the compartment, while there was a clear shift in prokaryotic composition. Some prokaryotic phyla were enriched in surface layers such as Proteobacteria, Euryarchaeota while others were mostly associated with deeper layers as Chloroflexi, Bathyarchaeota, Aminicenantes. Our results highlight the importance of considering fungal and prokaryotic counterparts for a better understanding of the microbial succession involved in plant organic matter decomposition in tropical coastal sediments.     

河口潮间带沉积物重金属累积及生态风险评价

于2015年7月份在闽江口鳝鱼滩湿地布设两条样带(T1和T2),并分别选取5个采样点采集沉积物样品。因重金属Co和V对动物和人类会造成一定危害,且闽江河口潮间带Co和V的研究较少,则对其理化性质、Co和V的空间分布特征以及污染程度等进行了研究,旨在为Co和V的污染研究提供参考。结果显示,该沉积物中Co和V的平均浓度分别为15.19 mg/kg、102.94 mg/kg,均高于福建省背景浓度,与其他河口对比,Co和V浓度处于中等水平。Co和V的含量由陆向海方向略有下降。地累积指数法分析得出沉积物中Co含量呈现轻度污染状态,V呈现无污染状态。此外,Co和V的潜在生态危害系数E_rⁱ分别为7.24—14.85和1.47—4.17,表明潜在生态危害轻微,闽江河口潮间带沉积物中Co和V属于轻度污染。     

Genomic mosaicism underlies the adaptation of marine Synechococcus ecotypes to distinct oceanic iron niches

Phytoplankton are limited by iron (Fe) in ~40% of the world's oceans including high-nutrient low-chlorophyll (HNLC) regions. While low-Fe adaptation has been well-studied in large eukaryotic diatoms, less is known for small, prokaryotic marine picocyanobacteria. This study reveals key physiological and genomic differences underlying Fe adaptation in marine picocyanobacteria. HNLC ecotype CRD1 strains have greater physiological tolerance to low Fe congruent with their expanded repertoire of Fe transporter, storage and regulatory genes compared to other ecotypes. From metagenomic analysis, genes encoding ferritin, flavodoxin, Fe transporters and siderophore uptake genes were more abundant in low-Fe waters, mirroring paradigms of low-Fe adaptation in diatoms. Distinct Fe-related gene repertories of HNLC ecotypes CRD1 and CRD2 also highlight how coexisting ecotypes have evolved independent approaches to life in low-Fe habitats. Synechococcus and Prochlorococcus HNLC ecotypes likewise exhibit independent, genome-wide reductions of predicted Fe-requiring genes. HNLC ecotype CRD1 interestingly was most similar to coastal ecotype I in Fe physiology and Fe-related gene content, suggesting populations from these different biomes experience similar Fe-selective conditions. This work supports an improved perspective that phytoplankton are shaped by more nuanced Fe niches in the oceans than previously implied from mostly binary comparisons of low- versus high-Fe habitats and populations.     

Crenarchaeota and Euryarchaeota in temperate estuarine sediments

AIMS: Application of molecular techniques to ecological studies has unveiled a wide diversity of micro-organisms in natural communities, previously unknown to microbial ecologists. New lineages of Archaea were retrieved from several non-extreme environments, showing that these micro-organisms are present in a large variety of ecosystems. The aim was therefore to assess the presence and diversity of Archaea in the sediments of the river Douro estuary (Portugal), relating the results obtained to ecological data. METHODS AND RESULTS: Total DNA was extracted from sediment samples obtained from an estuary deprived of vegetation, amplified by PCR and the resulting DNA fragments cloned. The archaeal origin of the cloned inserts was checked by Southern blot, dot blot or colony blot hybridization. Recombinant plasmids were further analysed by restriction with AvaII and selected for sequencing. Phylogenetic analyses of 14 sequences revealed the presence of members of the domain Archaea. Most of the sequences could be assigned to the kingdom Crenarchaeota. CONCLUSION: Most of these sequences were closely related to those obtained from non-extreme Crenarchaeota members previously retrieved from diverse ecosystems, such as freshwater and marine environments. SIGNIFICANCE AND IMPACT OF THE STUDY: The presence of archaeal 16S rDNA sequences in temperate estuarine sediments emerges as a valuable contribution to the understanding of the complexity of the ecosystem.     

Sources of organic carbon in mangrove sediments: variability and possible ecological implications

Mangrove sediments from three different mangrove ecosystems (Coringa Wildlife Sanctuary in the Godavari Delta, Andhra Pradesh, India, and Galle and Pambala, south-west Sri Lanka) were analysed for their organic carbon content, elemental ratios (C:N) and carbon stable isotope composition. Organic carbon content (0.6 – 31.7% dry weight), C/N ratios (7.0 – 27.3) and ¹³C (between –29.4 and –20.6) showed a wide range of values. Lower stocks of organic carbon coincided with low C/N (atom) ratios and less negative ¹³C values, indicating import of marine or estuarine particulate suspended matter. High organic carbon stocks coincided with high C/N ratios and ¹³C values close, but not equal, to those of the mangrove vegetation. The variations observed in this study and published literature data could be adequately described by a simple two-end mixing model, whereby marine/estuarine suspended matter and mangrove litter were taken as end members. Thus, while in some mangrove ecosystems or vegetation zones, organic carbon stocks can be very high and are almost entirely of mangrove origin, there also appear to be cases in which deposited estuarine or marine suspended matter is the dominant source of organic carbon and nitrogen in mangrove sediments. This situation is remarkably similar to that observed in temperate salt marsh ecosystems where the importance of local vascular plant production to the sediment organic carbon pool is equally variable. The observed high variability in organic matter origin is thought to have a major impact on the overall carbon dynamics in intertidal mangrove ecosystems.     

Overlap and partitioning of the ecological and isotopic niches

Recently, it was proposed that stable isotope patterns can be used to quantify the width of the ecological niche of animals. However, the potential effects of habitat use on isotopic patterns of consumers have not been fully explored and consequently isotopic patterns may yield deceptive estimates of niche width. Here, we simulated four different scenarios of a consumer foraging across an isotopically heterogeneous landscape to test the combined effects of habitat and diet selection on the widths of the isotopic niche. We then modeled the actions of a naïve researcher who randomly sampled consumers from the simulated populations, and used these results to assess the overlap and partitioning of the isotopic and the ecological niches when habitat‐derived differences among isotope signatures are not considered. Our results suggest that populations of dietary specialists exhibited broader isotopic niches than populations composed of dietary generalists, and habitat generalists exhibited narrower isotopic niche widths compared with populations of individuals that foraged in specific habitats. The conversion of isotopic niches to ecological niches without knowledge of foraging behavior and habitat‐derived isotopic differences transformed an informative δ‐space into ‘a blurry p‐space’. Therefore, knowledge of habitat‐derived differences in stable isotope values and understanding of habitat use and individual foraging behavior are critical for the correct quantification of the ecological niche.     

Paleoreconstruction of estuarine sediments reveal human‐induced weakening of coastal carbon sinks

Human activities in coastal areas frequently cause loss of benthic macrophytes (e.g. seagrasses) and concomitant increases in microalgal production through eutrophication. Whether such changes translate into shifts in the composition of sediment detritus is largely unknown, yet such changes could impact the role these ecosystems play in sequestrating CO₂. We reconstructed the sedimentary records of cores taken from two sites within Botany Bay, Sydney – the site of European settlement of Australia – to look for human‐induced changes in dominant sources of detritus in this estuary. Cores covered a period from the present day back to the middle Holocene (~6000 years) according to ²¹⁰Pb profiles and radiocarbon (¹⁴C) dating. Depositional histories at both sites could not be characterized by a linear sedimentation rate; sedimentation rates in the last 30–50 years were considerably higher than during the rest of the Holocene. C : N ratios declined and began to exhibit a microalgal source signature from around the time of European settlement, which could be explained by increased nutrient flows into the Bay caused by anthropogenic activity. Analysis of stable isotopic ratios of ¹²C/¹³C showed that the relative contribution of seagrass and C₃ terrestrial plants (mangroves, saltmarsh) to detritus declined around the time of rapid industrial expansion (~1950s), coinciding with an increase in the contribution of microalgal sources. We conclude that the relative contribution of microalgae to detritus has increased within Botany Bay, and that this shift is the sign of increased industrialization and concomitant eutrophication. Given the lower carbon burial efficiencies of microalgae (~0.1%) relative to seagrasses and C₃ terrestrial plants (up to 10%), such changes represent a substantial weakening of the carbon sink potential of Botany Bay – this occurrence is likely to be common to human‐impacted estuaries, and has consequences for the role these systems play in helping to mitigate climate change.     

Seasonal and substrate preferences of fungi colonizing leaves in streams: traditional versus molecular evidence

Aquatic hyphomycetes are the main fungal decomposers of plant litter in streams. We compared the importance of substrate (three leaf species, wood) and season on fungal colonization. Substrates were exposed for 12 4-week periods. After recovery, mass loss, fungal biomass and release of conidia by aquatic hyphomycetes were measured. Fungal communities were characterized by counting and identifying released conidia and by extracting and amplifying fungal DNA (ITS2), which was subdivided into phylotypes by denaturing gradient gel electrophoresis (DGGE) and terminal-restriction fragment length polymorphism (T-RFLP). Mass loss, fungal biomass and reproduction were positively correlated with stream temperature. Conidial diversity was highest between May and September. Numbers of different phylotypes were more stable. Principal coordinate analyses (PCO) and canonical analyses of principal coordinates (CAP) of presence/absence data (DGGE bands, T-RFLP peaks and conidial species) showed a clear seasonal trend (Por=0.88). Season was also a significant factor when proportional similarities of conidial communities or relative intensities of DGGE bands were evaluated (P相似文献   

Human neprilysin-2 (NEP2) and NEP display distinct subcellular localisations and substrate preferences

Neprilysin-2 (NEP2) is a novel metallopeptidase homologous to neprilysin (NEP), an enzyme involved in regulation of neuropeptide signalling. NEP2 exists as two alternatively spliced isoforms, NEP2 and NEP2(Delta). In this study, we cloned and expressed both human isoforms. Human NEP2 exists as a membrane-bound and soluble enzyme, whereas human NEP2(Delta) exists as two membrane-bound glycoforms, localised to the ER and plasma membrane. Surprisingly, NEP2 substrate specificity and inhibitor binding was distinct from that of human NEP, suggesting that NEP and NEP2 play distinct physiological roles in humans, and human NEP2 differs markedly from its rodent homologues.     

Hypersaline waters in salterns - natural ecological niches for halophilic black yeasts

Hypersaline waters in salterns have so far been considered to be populated only with halophilic algae and bacteria and completely lacking halophilic fungi. In this paper we present population dynamics of polymorphic black yeasts, isolated from hypersaline waters (3-30% NaCl) of a saltern, in relation to different physicochemical parameters. Hortaea werneckii, Phaeotheca triangularis, Trimmatostroma salinum, Aureobasidium pullulans and Cladosporium spp. were detected with the highest frequency just before the peak of halite (NaCl) concentration. Since H. werneckii, P. triangularis and T. salinum are not known outside saline environments, these results suggest that hypersaline water is their natural ecological niche.     

Diversity and significance of Burkholderia species occupying diverse ecological niches

Members of the genus Burkholderia are versatile organisms that occupy a surprisingly wide range of ecological niches. These bacteria are exploited for biocontrol, bioremediation and plant growth promotion purposes, but safety issues regarding human infections, especially in cystic fibrosis patients, have not been solved. This minireview gives an overview of the taxonomic and ecological diversity of the genus with particular emphasis on strains belonging to the Burkholderia cepacia complex and addresses the important question whether 'good' and 'bad' strains are actually the same.     

Bacterial activity and production in near-surface estuarine and freshwater sediments

Abstract: Two indices of bacterial production, thymidine incorporation and the frequency of divided and dividing cells were measured, along with a suite of measurements of aerobic and anaerobic bacterial activity, to investigate the relationship between bacterial cell production and organic carbon mineralisation at three different sediment sites: a sheltered intertidal estuarine mudflat (Kingoodie Bay), a riverside mudbank (Ashleworth Quay) and an intertidal mudflat in a hydraulically dynamic estuary (Aust Warth). Organic carbon mineralisation was dominated by anaerobic processes at all three sites: sulfate reduction at the two estuarine sites (equivalent to 76% and 61% of oxygen uptake) and methanogenesis at the freshwater site (56%). Although all three sites had similar bacterial population sizes, activities in Kingoodie Bay were 2–3 times higher than at Aust Warth or Ashleworth Quay. Thymidine incorporation rates and Numbers of Dividing and Divided Cells correlated strongly at all three sites. Thymidine incorporation rates were spatially uncoupled from zones of principal anaerobic activity, providing in situ evidence that sulfate-reducing bacteria and methanogens do not incorporate radiolabelled thymidine into DNA during growth. Cell yield was lower in the anaerobic zone, as subsurface peaks in anaerobic mineralisation were not matched by increases in bacterial productivity. However, as anaerobic degradation processes were so dominant, anaerobic productivity still accounted for the majority of cell production.     

Anaerobic reductive dechlorination of chlorinated dioxins in estuarine sediments

The biotransformation of 1,2,3,4-tetrachlorodibenzo-p-dioxin (1,2,3,4-tetraCDD) under anaerobic sulfate-reducing, methanogenic, and iron-reducing conditions was examined with anaerobic enrichment cultures established with sediment from an estuarine intertidal strait in the New York/New Jersey harbor. In addition, the effect of prior enrichment on 2-bromophenol or a mixture of 2-, 3-, and 4-bromophenol on dioxin dechlorination was examined. All enrichments were spiked with 1 ppm 1,2,3,4-tetraCDD and monitored by gas chromatography-mass spectrometry for up to a 3-year period. Reductive dechlorination was initially observed only under methanogenic conditions in the cultures enriched on all three bromophenol isomers. 1,2,3,4-TetraCDD was dechlorinated in the lateral position to 1,2,4-triCDD. The initial appearance of 1,2,4-triCDD was observed after 2 months, with further dechlorination to 1,3-diCDD within 17 months.     

Development of a quantitative method for detecting enteroviruses in estuarine sediments.

Several investigators have reported on the detection of enteric viruses in marine sediments, but none determined the efficiency of their methods and only limited volumes of sediment were sampled. The purpose of this investigation was to develop a quantitative method for detecting enteroviruses in marine sediments so that their relative proportion to viruses freely suspended in estuarine water could be more accurately determined. Poliovirus was found to adsorb readily to natural marine sediments collected along the Texas Gulf coast. A number of substances were evaluated for their ability to elute adsorbed viruses. A solution of 10% fetal calf serum adjusted to pH 10.5 and 0.05M ethylenediaminetetraacetate (pH 11.0) were found to be the best eluents. Using ethylenediaminetetraacetate as an eluent, it was possible to elute virus from large volumes of sediment and reconcentrate the sediment eluate into an economically assayable volume (30 to 50 ml). Poliovirus could be recovered from the sediment with an overall efficiency of 50%. This method was found to be satisfactory for the recovery of naturally occurring animal viruses in estuarine sediments from the upper Texas Gulf coast.     

Development of a quantitative method for detecting enteroviruses in estuarine sediments.

Several investigators have reported on the detection of enteric viruses in marine sediments, but none determined the efficiency of their methods and only limited volumes of sediment were sampled. The purpose of this investigation was to develop a quantitative method for detecting enteroviruses in marine sediments so that their relative proportion to viruses freely suspended in estuarine water could be more accurately determined. Poliovirus was found to adsorb readily to natural marine sediments collected along the Texas Gulf coast. A number of substances were evaluated for their ability to elute adsorbed viruses. A solution of 10% fetal calf serum adjusted to pH 10.5 and 0.05M ethylenediaminetetraacetate (pH 11.0) were found to be the best eluents. Using ethylenediaminetetraacetate as an eluent, it was possible to elute virus from large volumes of sediment and reconcentrate the sediment eluate into an economically assayable volume (30 to 50 ml). Poliovirus could be recovered from the sediment with an overall efficiency of 50%. This method was found to be satisfactory for the recovery of naturally occurring animal viruses in estuarine sediments from the upper Texas Gulf coast.     

Identifying and understanding ecological preferences for habitat or prey

Patchy, non-random associations of species with habitats and of consumers with particular types of food are commonly found in the ecological literature. In many cases, these patterns are reported to show some preference by an animal making choices about its environment. Generally, however, what is reported is simply the pattern of association and the process that gives rise to this pattern is not further examined. Nevertheless, there are numerous concepts that need to be considered simply to demonstrate the pattern, including the spatial and temporal scales at which the observations are made. When animals make choices between two objects, it is difficult to separate out potential negative, neutral or positive responses to either or both of the objects, without well thought-out manipulative experiments. Apparent preference for food may be influenced by “catchability” or “acceptability” of the prey and/or the past history of the consumer and the experiments to separate these effects are naturally complex. Many experiments examining preferences are beset by problems of non-independence and lack of appropriate controls, which makes them difficult to interpret. This review introduces some of the logical, conceptual, experimental and statistical problems that beset many studies of preference and proposes important steps that must be considered in further studies to unravel this fascinating topic.