Experimental Evidence on Nutrient and Substrate Limitation of Baltic Sea sea-ice Algae and Bacteria

The effect of nutrient limitation on Baltic Sea ice algae, and substrate and nutrient limitation on ice bacteria, was studied in a series of in situ -experiments conducted during the winter of 2002 in northern Baltic Sea. Community level changes in algal biomass (chlorophyll a) and productivity, and bacterial thymidine and leucine incorporation were followed for one week after the addition of nutrient and/or organic carbon rich filtered seawater to the experimental units. The results showed the major contribution of snow cover to the algal responses during the beginning of the ice-covered season. Algal communities were able to grow even in January if no snow was present. Nutrient addition did occasionally have an effect on algal biomass and productivity in the ice. Surprisingly, seeding effect from the ice to the underlying water was negatively affected by the nutrient availability in March. Bacterial limitation varied between nutrient (phosphorus) and substrate limitations. The results showed, that limitation in both algal and bacterial communities changed periodically in the northern Baltic Sea ice.     

Autotrophic Ammonia-Oxidizing Bacteria Contribute Minimally to Nitrification in a Nitrogen-Impacted Forested Ecosystem

Deposition rates of atmospheric nitrogenous pollutants to forests in the San Bernardino Mountains range east of Los Angeles, California, are the highest reported in North America. Acidic soils from the west end of the range are N-saturated and have elevated rates of N-mineralization, nitrification, and nitrate leaching. We assessed the impact of this heavy nitrogen load on autotrophic ammonia-oxidizing communities by investigating their composition, abundance, and activity. Analysis of 177 cloned β-Proteobacteria ammonia oxidizer 16S rRNA genes from highly to moderately N-impacted soils revealed similar levels of species composition; all of the soils supported the previously characterized Nitrosospira clusters 2, 3, and 4. Ammonia oxidizer abundance measured by quantitative PCR was also similar among the soils. However, rates of potential nitrification activity were greater for N-saturated soils than for soils collected from a less impacted site, but autotrophic (i.e., acetylene-sensitive) activity was low in all soils examined. N-saturated soils incubated for 30 days with ammonium accumulated additional soluble ammonium, whereas less-N-impacted soils had a net loss of ammonium. Lastly, nitrite production by cultivated Nitrosospira multiformis, an autotrophic ammonia-oxidizing bacterium adapted to relatively high ammonium concentrations, was significantly inhibited in pH-controlled slurries of sterilized soils amended with ammonium despite the maintenance of optimal ammonia-oxidizing conditions. Together, these results showed that factors other than autotrophic ammonia oxidizers contributed to high nitrification rates in these N-impacted forest soils and, unlike many other environments, differences in nitrogen content and soil pH did not favor particular autotrophic ammonia oxidizer groups.     

Root-Associated Bacteria Contribute to Mineral Weathering and to Mineral Nutrition in Trees: a Budgeting Analysis

The principal nutrient source for forest trees derives from the weathering of soil minerals which results from water circulation and from plant and microbial activity. The main objectives of this work were to quantify the respective effects of plant- and root-associated bacteria on mineral weathering and their consequences on tree seedling growth and nutrition. That is why we carried out two column experiments with a quartz-biotite substrate. The columns were planted with or without pine seedlings and inoculated or not with three ectomycorrhizosphere bacterial strains to quantify biotite weathering and pine growth and to determine how bacteria improve pine growth. We showed that the pine roots significantly increased biotite weathering by a factor of 1.3 for magnesium and 1.7 for potassium. We also demonstrated that the inoculation of Burkholderia glathei PML1(12) significantly increased biotite weathering by a factor of 1.4 for magnesium and 1.5 for potassium in comparison with the pine alone. In addition, we observed a significant positive effect of B. glathei PMB1(7) and PML1(12) on pine growth and on root morphology (number of lateral roots and root hairs). We demonstrated that PML1(12) improved pine growth when the seedlings were supplied with a nutrient solution which did not contain the nutrients present in the biotite. No improvement of pine growth was observed when the seedlings were supplied with all the nutrients necessary for pine growth. We therefore propose that the growth-promoting effect of B. glathei PML1(12) mainly resulted from the improved plant nutrition via increased mineral weathering.     

High Diversity of Extended-Spectrum Beta-Lactamase-Producing Bacteria in an Urban River Sediment Habitat

Antibiotic-resistant bacteria (ARB) have been surveyed widely in water bodies, but few studies have determined the diversity of ARB in sediment, which is the most taxon-abundant habitat in aquatic environments. We isolated 56 extended-spectrum β-lactamase (ESBL)-producing bacteria from a single sediment sample taken from an urban river in China. All strains were confirmed for ESBL-producing capability by both the clavulanic acid combination disc method and MIC determination. Of the isolated strains, 39 were classified as Enterobacteriaceae (consisting of the genera Escherichia, Klebsiella, Serratia, and Aeromonas) by 16S rRNA gene sequencing and biochemical analysis. The present study identifies, for the first time, ESBL-producing strains from the families Brucellaceae and Moraxellaceae. The bla_CTX-M gene was the most dominant of the ESBL genes (45 strains), while the bla_TEM gene was the second-most dominant (22 strains). A total of five types of bla_CTX-M fragments were identified, with both known and novel sequences. A library of bla_CTX-M cloned from the sediment DNA showed an even higher diversity of bla_CTX-M sequences. The discovery of highly diverse ESBL-producing bacteria and ESBL genes, particularly bla_CTX, in urban river sediment raises alarms for potential dissemination of ARB in communities through river environments.Antibiotic-resistant bacteria (ARB) have been found widely in aquatic environments (1, 18, 24). ARB in rivers may originate from anthropogenic sources, such as hospital, municipal, and aquaculture effluents (3, 16, 23); in addition, they could occur naturally, since many acquired resistance mechanisms originated in producers of antibiotics, such as actinomycetes (12). Both anthropogenic and naturally occurring ARB in water environments may compromise human health, since people may be infected by ARB through drinking water, aquatic products, and direct contact with water bodies. Moreover, the ARB may transfer the antibiotic resistance genes to other pathogens through horizontal gene transfer (1).Sediment has the highest microbial diversity in water environments. The species richness and abundance of the sediment community are comparable to those of soil and are orders of magnitude higher than those of the planktonic community in the upper water layer (10, 20). It is reasonable to deduce that a wide variety of ARB might exist in sediment environments, as they are taxon-rich habitats, particularly in sediments receiving wastewater. Nevertheless, despite extensive studies surveying ARB in water columns, the diversity of antibiotic resistance in sediment environments has seldom been investigated.The present study therefore focused on an urban river sediment environment as a model, concentrating on the diversity of extended-spectrum β-lactamase (ESBL)-producing bacteria. ESBL-producing organisms have been emerging both in nosocomial and in community settings since the 1980s (4, 13, 14). In aquatic environments, ESBL-producing bacteria have been found in sewage and water samples (11, 13, 16), but their diversity in sediment habitats has never been analyzed before. In the present study, the diversity of ESBL-producing organisms was studied by both culture-dependent and culture-independent methods. A wide variety of ESBL-producing bacteria were isolated using a vast array of different nutrient media. The ESBL-producing abilities of the isolated strains were determined by both the clavulanic acid combination disc method and MIC determination. ESBL genes were identified and characterized by PCR and sequencing. A clone library of the bla_CTX-M gene, which was the most abundant type of ESBL gene found in the isolated bacteria, was cloned directly from the sediment and sequenced. The data revealed a diverse community of ESBL-producing bacteria that exists in urban aquatic sediment.     

Solutions to Problems in Enumerating Sediment Bacteria by Direct Counts

We examined the effect of different sediment types on the staining effectiveness of the fluorochrome DAPI (4′-6-diamidino-2-phenylindole dihydrochloride) over a wide range of concentrations and on the masking effect of sediment particles on DAPI-stained bacteria. Sediment type greatly affects the staining efficiency of DAPI, and most published studies seem to have underestimated bacterial abundances by using suboptimal concentrations of the fluorochrome. A DAPI concentration of 5 μg ml⁻¹ is required to effectively stain the bacteria in most sediments that can be sampled with a gravity corer. When the sediments are diluted 687 times (a dilution factor similar to those most often used in the literature), sediment particle masking of stained bacteria is highly variable for different sediment types. By using a measure of turbidity (A₇₅₀) to indicate masking and the quartz-corrected water content as a measure of the initial (in situ) dilution of each sediment type, it becomes possible to show a linear relationship between masking and the integrated (initial × experimental) dilution of various sediments. This relationship allows the development of a correction procedure for masking which makes accurate and unbiased counts possible. Data so obtained show a strong relationship between bacteria (cells per milliliter of fresh sediment) and sediment organic matter (grams [dry weight] per milliliter of fresh sediment), one that is not discernable without the correction. The proposed method of staining and correction for sediment masking provides the basis for a standardized interpretation of sediment bacterial counts.     

Nutrient and Sediment Retention in a Temperate Marsh Ecosystem

The Wye marsh, an undeveloped wetland of 639.9 ha, serves as a receiving water for a 19,600 ha agricultural watershed before discharging into the Great Lakes. Seasonal and diel changes in limnological variables, most notably nitrogen, phosphorus, silica and turbidity, have been examined in the Wye river, marsh and discharge waters over an 11-month period and related to the composition of marsh sediments. Retention rates of the marsh ecosystem for incoming nutrients and suspended solids have been estimated by calculations of mean monthly inflow to outflow ratios using the levels of these factors in the Wye River and the marsh discharge. Calculated mean monthly retention rates of the marsh for incoming nutrients is estimated at no less than 61% for nitrogen-N, 36% for total phosphate, and 14% for soluble silica during the ice-free period. Based on observed turbidity levels, the retention of incoming suspended solids is estimated at 65% for the same period. The Wye marsh is a substantial sump for inorganic and organic materials which are retained within the water column, biomass and unconsolidated sediments.     

Evidence for Detachment of Indigenous Bacteria from Aquifer Sediment in Response to Arrival of Injected Bacteria

Two bacterial strains isolated from the aquifer underlying Oyster, Va., were recently injected into the aquifer and monitored using ferrographic capture, a high-resolution immunomagnetic technique. Injected cells were enumerated on the basis of a vital fluorescence stain, whereas total cell numbers (stained target cells plus unstained target and antigenically similar indigenous bacteria) were identified by cell outlines emanating from fluorophore-conjugated antibodies to the two target strains. The arrival of injected bacteria at the majority of monitored sampling ports was accompanied by simultaneous temporary increases in unstained cell counts that outnumbered the injected bacteria by 2- to 100-fold. The origin and mechanism of appearance of the unstained cells are considered.     

Lithotrophic and Heterotrophic Bacteria in Deep Subsurface Sediments and Their Relation to Sediment Properties

Subsurface sediments obtained from three cores drilled to depths of 260 m below the surface in South Carolina were analyzed for heterotrophic bacteria; N₂‐fixing microaerophiles; and nitrifying, sulfur‐oxidizing, and H₂‐oxidizing lithotrophic bacteria. In addition, pore waters were extracted for chemical analysis of inorganic nitrogen species, sulfate, dissolved organic carbon, pH, and Eh. Autotroph populations were generally less than 10³ most probable number (MPN) g^‐1 dry sediment with sulfur‐oxidizing bacteria, detected in 60% of the sediment samples, being the most frequently encountered group. Nitrifying bacteria were detected mainly in sediments from one borehole (P28), and their populations in those sediments were correlated with pore‐water ammonium concentrations. Populations of heterotrophic bacteria in 60% of the sediments were greater than 10⁶ colony forming units (CFU) g^‐1 dry sediment and were typically lower in sediments of high clay content and low pH. Microaerophilic N₂‐fixing bacteria were cultured from >50% and bacteria capable of growth on H₂ were cultured from 35% of the subsurface sediments examined. Sediment texture, which controls porosity, water potential, and hydraulic conductivity, appears to be a major factor influencing microbial populations in coastal plain subsurface sediments.     

Transmembrane Transport and Release of GABA in the Brain of Rats Subjected to Postnatal Hypoxia

We studied the effects of early postnatal hypoxia on the efficiency of active GABA transport through the plasma membrane of synaptic terminals (synaptosomes) isolated from the cerebral cortex, hippocampus, and thalamus of rats and on non-stimulated and Ca²⁺-stimulated GABA release. The state of hypoxia was induced by exposure of 10- to 12-day-old rats to a respiratory medium with low O₂ content (4% О₂ and 96% N₂) for 12 min (up to the initiation of clonico-tonic seizures). Animals were taken in the experiment 8 to 9 weeks after an episode of hypoxic stress. The intensity of transmembrane transport of GABA was estimated according to accumulation of [³Н]GABA in a coarse synaptosomal fraction. The process was characterized by calculation of the Michaelis constant K _m and also of the initial (within the 1st min) and maximum rates of accumulation of [³Н]GABA. The means of the initial rate of [³Н]GABA accumulation in preparations from the thalamus, cortex, and hippocampus were 205.5 ± 8.8, 266.2 ± 29.6, and 302.3 ± 31.2 pmol/min⋅mg protein, respectively. Hypoxic stress influenced the rates of accumulation of [³Н]GABA in synaptic terminals from the cortex and hippocampus but not in those from the thalamus. According to the characteristics of the response to hypoxic stress, all experimental animals could be classified into two groups. In some rats, accumulation of [³Н]GABA in both cortical and hippocampal synaptosomes decreased insignificantly (by about 15%), while in other animals this parameter increased significantly (by nearly 50%) for the cortex and decreased by 21.5%, on average, for the hippocampus. The affinity of the transporter with respect to [³Н]GABA in the cortex and hippocampus was nearly the same and showed no changes under the influence of hypoxia. The non-stimulated release of [³Н]GABA after the influence of hypoxia increased in all structures, while the depolarization-induced Ca²⁺-dependent release of [³Н]GABA was intensified only in synaptosomes from the cerebral cortex. The mechanisms of development of modifications of GABA-ergic processes under the influence of hypoxic stress in the course of the perinatal period are discussed. Neirofiziologiya/Neurophysiology, Vol. 40, No. 4, pp. 293–302, July–August, 2008.     

Synaptosomal Uptake and Release of Dopamine in Rat Striatum After Hypoxia

Hypoxia induces alterations of central monoaminergic transmission and of behavior. We studied the effect of hypoxia on adult and newborn rats to obtain more information about long-lasting changes of dopamine (DA) transmission caused by neonatal hypoxia. One single exposure of adult rats to hypoxia leads to short-term alterations of DA uptake: decreased affinity of the uptake carrier to DA (Km, 269.5% versus control) and a sharp increase of Vmax up to 301.4% resulting in an increase of total uptake of DA into the striatum synaptosomes. The K+-evoked DA release decreased to 69.5%. After 1 week of recovery all parameters are normalized. Chronic postnatal hypoxia (postnatal day 2-11) caused long-lasting changes of DA release and uptake opposite to those observed in adult rats. Three months after hypoxia, the K+-stimulated DA release was enhanced (132% of control), and the uptake was reduced due to decreased affinity of the uptake carrier system for the substrate (Km, 187% of control value). In conclusion, the alterations observed after chronic postnatal hypoxia reflect special adaptive processes that are related to the high plasticity of the immature neonatal brain and contribute to an increased DA function in the nigrostriatal system.     

Soil Charcoal in Old-Growth Rain Forests from Sea Level to the Continental Divide

Soil charcoal is an indicator of Holocene fires as well as a palaeoecological signature of pre-Colombian land use in Neotropical rain forests. To document rain forest fire history, we examined soil charcoal patterns in continuous old-growth forests along an elevational transect from sea level to the continental divide on the Atlantic slope of Costa Rica. At 10 elevations we sampled 1-ha plots, using 16 cores/ha to collect 1.5-m deep soil samples. We found charcoal in soils at every elevation, with total dry mass ranging from 3.18 g/m² at 2000-m elevation to as much as 102.7 g/m² at 300 m. Soil charcoal is most abundant at the wettest lowland sites (60–500 m) and less at montane elevations (> 1000 m) where there is less rainfall. Between 30- and 90-cm soil depth, soil charcoal is present consistently and every 1-ha plot has charcoal evidence for multiple fire events. Radiocarbon dates range from 23,240 YBP at 1750-m elevation to 140 YBP at 2600 m. Interestingly, none of the charcoal samples from 2600 m are older than 170 yr, which suggests that forests near the continental divide are relatively young replacement stands that have re-established since the most recent localized volcanic eruption on Volcán Barva. We propose that these old-growth forests have been disturbed infrequently but multiple times as a consequence of anthropogenic and natural fires.     

Anaerobic Ammonia-Oxidizing Bacteria and Related Activity in Baltimore Inner Harbor Sediment

The discovery of bacteria capable of anaerobic ammonia oxidation (anammox) has generated interest in understanding the activity, diversity, and distribution of these bacteria in the environment. In this study anammox activity in sediment samples obtained from the Inner Harbor of Baltimore, Md., was detected by ¹⁵N tracer assays. Anammox-specific oligonucleotide primer sets were used to screen a Planctomycetales-specific 16S rRNA gene library generated from sediment DNA preparations, and four new anammox bacterial sequences were identified. Three of these sequences form a cohesive new branch of the anammox group, and the fourth sequence branches separately from this group. Denaturing gradient gel electrophoresis analysis of sediment incubated with anammox-specific media confirmed the presence of the four anammox-related 16S rRNA gene sequences. Evidence for the presence of anammox bacteria in Inner Harbor sediment was also obtained by using an anammox-specific probe in fluorescence in situ hybridization studies. To our knowledge, this is the first report of anammox activity and related bacterial 16S rRNA gene sequences from the Chesapeake Bay basin area, and the results suggest that this pathway plays an important role in the nitrogen cycle of this estuarine environment. Furthermore, the presence of these bacteria and their activity in sediment strengthen the contention that anammox-related Plactomycetales are globally distributed.     

From Bacteria to Fish: Ecological Consequences of Seasonal Hypoxia in a Great Lakes Estuary

The occurrence of bottom-water hypoxia is increasing in bodies of water around the world. Hypoxia is of concern due to the way it negatively impacts lakes and estuaries at the whole ecosystem level. During 2015, we examined the influence of hypoxia on the Muskegon Lake ecosystem by collecting surface- and bottom-water nutrient samples, bacterial abundance counts, benthic fish community information, and performing profiles of chlorophyll and phycocyanin as proxies for phytoplankton and cyanobacterial growth, respectively. Several significant changes occurred in the bottom waters of the Muskegon Lake ecosystem as a result of hypoxia. Lake-wide concentrations of soluble reactive phosphorus (SRP) and total phosphorus increased with decreasing dissolved oxygen (DO). Bacterial abundance was significantly lower when DO was less than 2.2 mg L^?1. Whereas there were no drastic changes in surface chlorophyll a concentration through the season, phycocyanin increased threefold during and following a series of major wind-mixing events. Phycocyanin remained elevated for over 1.5 months despite several strong wind events, suggesting that high SRP concentrations in the bottom waters may have mixed into the surface waters, sustaining the bloom. The fish assemblage in the hypolimnion also changed in association with hypoxia. Overall fish abundance, number of species, and maximum length all decreased in catch as a function of bottom DO concentrations. The link between hypoxia and wind events appears to serve as a positive feedback loop by continuing internal loading and cyanobacterial blooms in the lake, while simultaneously eroding habitat quality for benthic fish.     

Flagella-Mediated Adhesion and Extracellular DNA Release Contribute to Biofilm Formation and Stress Tolerance of Campylobacter jejuni

Campylobacter jejuni is a leading cause of foodbourne gastroenteritis, despite fragile behaviour under standard laboratory conditions. In the environment, C. jejuni may survive within biofilms, which can impart resident bacteria with enhanced stress tolerance compared to their planktonic counterparts. While C. jejuni forms biofilms in vitro and in the wild, it had not been confirmed that this lifestyle confers stress tolerance. Moreover, little is understood about molecular mechanisms of biofilm formation in this pathogen. We previously found that a ΔcprS mutant, which carries a deletion in the sensor kinase of the CprRS two-component system, forms enhanced biofilms. Biofilms were also enhanced by the bile salt deoxycholate and contained extracellular DNA. Through more in-depth analysis of ΔcprS and WT under conditions that promote or inhibit biofilms, we sought to further define this lifestyle for C. jejuni. Epistasis experiments with ΔcprS and flagellar mutations (ΔflhA, ΔpflA) suggested that initiation is mediated by flagellum-mediated adherence, a process which was kinetically enhanced by motility. Lysis was also observed, especially under biofilm-enhancing conditions. Microscopy suggested adherence was followed by release of eDNA, which was required for biofilm maturation. Importantly, inhibiting biofilm formation by removal of eDNA with DNase decreased stress tolerance. This work suggests the biofilm lifestyle provides C. jejuni with resilience that has not been apparent from observation of planktonic bacteria during routine laboratory culture, and provides a framework for subsequent molecular studies of C. jejuni biofilms.     

Sediment Distribution of Methanogenic Bacteria in Lake Erie and Cleveland Harbor

The direct fluorescent-antibody technique was employed to determine the distribution patterns of four species of methanogens in the sediments of Lake Erie and Cleveland Harbor. Methanobacterium ruminantium was the most numerous methanogen found in regions of high-organic-silt sediments. The population of this species ranged from 10⁶ to 10⁹ cells/g of dry sediment. Methanobacterium strain MoH and Methanosarcina barkeri were identified in sand-silt, clay, or sand sediments. These methanogens ranged in density from 10⁶ to 10⁷ cells/g of dry sediment. Methanospirillum hungatii was observed only after an organic enrichment was performed on Cleveland Harbor sediments. The seasonal and selective sediment distribution of these methanogens appears to be related to the type and concentration of carbon as substrate as well as to the activities of heterotrophic and sulfate-reducing bacteria.     

Changes in Sediment Bacterial Community in Response to Long-Term Nutrient Enrichment in a Subtropical Seagrass-Dominated Estuary

Florida Bay exhibits a natural gradient of strong P limitation in the east which shifts to weak P or even N limitation at the western boundary. This nutrient gradient greatly affects seagrass abundance and productivity across the bay. We assessed the effects of N and P additions on sediment bacterial community structure in relation to the existing nutrient gradient in Florida Bay. Sediment samples from 24 permanent 0.25 m² plots in each of six sites across Florida Bay were fertilized with granular N and P in a factorial design for 26 months. Sediment bacterial community structure was analyzed using PCR-denaturing gradient gel electrophoresis (DGGE) analysis of 16S ribosomal RNA (rRNA) genes and a cloning strategy from DGGE bands. The phylogenetic positions of 16S rRNA sequences mostly fell into common members found in marine sediments such as sulfate-reducing Deltaproteobacteria, Gammaproteobacteria, Spirochaetes, and Bacteriodetes. Twenty-eight common DGGE bands were found in all sediment samples; however, some DGGE bands were only found or were better represented in eastern sites. Bacterial community diversity (Shannon-Weiner index) showed similar values throughout all sediment samples. The N treatment had no effect on the bacterial community structures across the bay. Conversely, the addition of P significantly influenced the bacterial community structure at all but the most western site, where P is least limiting due to inputs from the Gulf of Mexico. P additions enhanced DGGE band sequences related to Cytophagales, Ectothiorhodospiraceae, and Desulfobulbaceae, suggesting a shift toward bacterial communities with increased capability to degrade polymeric organic matter. In addition, a band related to Deferribacteres was enhanced in eastern sites. Thus, indigenous environmental conditions were the primary determining factors controlling the bacterial communities, while the addition of P was a secondary determining factor. This P-induced change in community composition tended to be proportional to the amount of P limitation obviated by the nutrient additions.     

泉古菌醇与绿素在东海陆架区的分布及关系研究

【目的】研究东海陆架地区的沉积物中的泉古菌醇、绿素的分布及其相关关系。【方法】通过有机化学的方法将泉古菌醇和绿素从沉积物中萃取出来之后,利用高效液相色谱质谱连用对泉古菌醇进行定量检测,利用高效液相色谱对绿素进行定量检测。【结果】泉古菌醇和绿素在长江河口绝对量的分布在空间上呈现类似关系,并且受到陆源输入的影响较小。【结论】东海陆架区的泉古菌醇和绿素均为海洋产生,而非陆源输入,且两者呈现明显的相关关系,提示泉古菌醇具有指示历史时期东海表层初级生产力变化的潜在应用。