Bacterial Heterotrophy Research Articles

Dissolved carbohydrates and its influence on bacterioplankton diversity in the euphotic zone of Equatorial Indian Ocean during southwest monsoon

The Equatorial Indian Ocean (EIO) is oligotrophic in nature, low in productivity and characterised by relatively high bacterial biomass and heterotrophic productivity. The microbial biomass is fuelled by dissolved organic carbon (DOC) whose lability depends upon its chemistry. During an expedition in the EIO, samples for dissolved carbohydrates (DCHO), dissolved monosaccharide (MCHO), dissolved polysaccharide (PCHO), total bacterial abundance, total organic carbon (TOC), nutrients, chlorophyll a (chl a), bacterial diversity, and phytoplankton composition were estimated along two transects (TS-1 & TS-2) in the euphotic depth (200 m). DCHO and MCHO samples were analysed using 3-methyl-2-benzothiozolinone hydrazone hydrochloride (MBTH) method. The DCHO, MCHO, and PCHO concentrations in TS-1 ranged from 2.4 to 5.8 μM; 0.7 to 2.7 μM; 0.7 to 3.4 μM, while in TS-2 it ranged from 2.2 to 4.8 μM; 0.3 to 2.8 μM; 0.2 to 3.8 μM, respectively. Vertically, DCHO concentrations decreased within the photic depths in most stations. PCHO concentrations were relatively greater in TS-2 than TS-1, which may be due to preferential removal of MCHO in TS-2. In the top 200 m of the water column, Proteobacteria was the most abundant bacterial phylum followed by Cyanobacteria, Actinobacteriota, Bacteroidota, and SAR-324 while dinoflagellates dominated the phytoplankton population. The distribution of DCHO and PCHO were inversely correlated to salinity, temperature, and chl a. The bacterial heterotrophs like alpha-Proteobacteria, Chloroflexii, and Verrumicrobiota along with SAR324 and Actinobacteriota were clustered with nutrients, while Bdellovibriota and Dadabacteria clustered with MCHO, PCHO, and DCHO. These results highlight the impact of DCHO & PCHO lability on the distribution of bacterial community and delineate oceanographic factors that regulate the distribution of DCHO and its constituents in EIO waters.

Biomass losses of Sodalinema alkaliphilum in alkaline, high pH, open raceway ponds

Growing cyanobacteria in high pH (10+), high carbonate alkalinity medium (0.5 M) increases the driving force for CO2 capture and helps exclude competitors and predators. But in these conditions, cyanobacteria might expend more energy to maintain osmotic gradients across their membrane. Thus, these extremophiles may respire more fixed carbon, increasing biomass losses compared to growth in milder conditions. In this work, a microbial consortium primarily composed of Sodalinema alkaliphilum (formerly Phormidium alkaliphilum) from alkaline soda lakes was grown in an outdoor open raceway pond. Night-time biomass losses were ca. 5 % by mass. Stable isotope probing (SIP) found respiration accounted for 0–2 % of daily biomass losses with no detectable difference in respiration rates between day and night. Comparisons of SIP and mass density measurements indicated respiration was not always the primary driver of biomass loss and that DOC release may contribute, even during stable operation. Proteomics and 16S rRNA DNA sequencing showed the abundance of bacterial heterotrophs was low with Cyclonatronum spp. representing the largest fraction (<1 %). The relative abundance of proteins within the S. alkaliphilum proteome was stable but the rate of protein synthesis varied. Overall rates of protein synthesis were highest in the afternoon (when photosynthesis was most active), but quality control proteins were preferentially made in the morning, likely in preparation for the work ahead. Understanding when and how biomass is lost in cultivation systems is crucial in informing efforts to improve biomass models and enhance biomass yield.

Compound-specific carbon isotope measurements of individual lipid biomarkers from immature Ediacaran rocks of Baltica

Compound-specific carbon isotope ratios (CSIA) were measured for a suite of lipid biomarker compounds extracted from immature, late Ediacaran sedimentary rocks from drill cores sampled across Baltica. Using a newly developed picomolar‐scale CSIA (pico‐CSIA) method, we measured carbon isotope compositions of the abundant n-alkanes and hopanes, as well as C29 sterane, pristane, and phytane. Total organic carbon (TOC) of the Kotlin Regional Horizon in Baltica (Saint Petersburg area, Utkina Zavod drill core), from a low-salinity coastal environment, is consistently enriched in 13C by up to 10‰, compared to that for Redkino and Kotlin marine rocks from other locations in Baltica. This 13C enrichment is also recorded by the n-alkanes, hopanes, phytane, and C29 sterane. In all locations, the δ13C values of the C29 sterane are within 2‰ of the bacterial hopane δ13C values and within 0.7‰ of δ13CTOC, suggesting that the abundant hopanes within these sediments could be derived from RuBisCO Calvin-Benson-Bassham pathway-utilizing organisms, as well as from bacterial heterotrophs. Since δ13Clipid signature tracks δ13CTOC values for the Kotlin Regional Horizon samples from Utkina Zavod location, the significant 13C enrichments in this interval reflect either the δ13C composition of DIC used for autotrophy or a muted magnitude of carbon isotope fractionation during lipid biosynthesis, but are not due to enhanced preservation of organic compounds and geopolymers derived from 13C-enriched biochemicals. Pico-CSIA and biomarker data provide evidence for both regional environmental heterogeneity and secular changes in carbon cycling during deposition of sediments of the Kotlin and Redkino Regional Horizon intervals.

Cryptic Diversity of Black Band Disease Cyanobacteria in Siderastrea siderea Corals Revealed by Chemical Ecology and Comparative Genome-Resolved Metagenomics.

Black band disease is a globally distributed and easily recognizable coral disease. Despite years of study, the etiology of this coral disease, which impacts dozens of stony coral species, is not completely understood. Although black band disease mats are predominantly composed of the cyanobacterial species Roseofilum reptotaenium, other filamentous cyanobacterial strains and bacterial heterotrophs are readily detected. Through chemical ecology and metagenomic sequencing, we uncovered cryptic strains of Roseofilum species from Siderastrea siderea corals that differ from those on other corals in the Caribbean and Pacific. Isolation of metabolites from Siderastrea-derived Roseofilum revealed the prevalence of unique forms of looekeyolides, distinct from previously characterized Roseofilum reptotaenium strains. In addition, comparative genomics of Roseofilum strains showed that only Siderastrea-based Roseofilum strains have the genetic capacity to produce lasso peptides, a family of compounds with diverse biological activity. All nine Roseofilum strains examined here shared the genetic capacity to produce looekeyolides and malyngamides, suggesting these compounds support the ecology of this genus. Similar biosynthetic gene clusters are not found in other cyanobacterial genera associated with black band disease, which may suggest that looekeyolides and malyngamides contribute to disease etiology through yet unknown mechanisms.

Growth-stage-related shifts in diatom endometabolome composition set the stage for bacterial heterotrophy

Phytoplankton-derived metabolites fuel a large fraction of heterotrophic bacterial production in the global ocean, yet methodological challenges have limited our understanding of the organic molecules transferred between these microbial groups. In an experimental bloom study consisting of three heterotrophic marine bacteria growing together with the diatom Thalassiosira pseudonana, we concurrently measured diatom endometabolites (i.e., potential exometabolite supply) by nuclear magnetic resonance (NMR) spectroscopy and bacterial gene expression (i.e., potential exometabolite uptake) by metatranscriptomic sequencing. Twenty-two diatom endometabolites were annotated, with nine increasing in internal concentration in the late stage of the bloom, eight decreasing, and five showing no variation through the bloom progression. Some metabolite changes could be linked to shifts in diatom gene expression, as well as to shifts in bacterial community composition and their expression of substrate uptake and catabolism genes. Yet an overall low match indicated that endometabolome concentration was not a good predictor of exometabolite availability, and that complex physiological and ecological interactions underlie metabolite exchange. Six diatom endometabolites accumulated to higher concentrations in the bacterial co-cultures compared to axenic cultures, suggesting a bacterial influence on rates of synthesis or release of glutamate, arginine, leucine, 2,3-dihydroxypropane-1-sulfonate, glucose, and glycerol-3-phosphate. Better understanding of phytoplankton metabolite production, release, and transfer to assembled bacterial communities is key to untangling this nearly invisible yet pivotal step in ocean carbon cycling.

Microbial contribution to post-fire tundra ecosystem recovery over the 21st century

Tundra ecosystems have experienced an increased frequency of fire, and this trend is predicted to continue throughout the 21st Century. Post-fire recovery is underpinned by complex interactions between microbial functional groups that drive nutrient cycling. Here we use a mechanistic model to demonstrate an acceleration of the nitrogen cycle post-fire driven by changes in niche space and microbial competitive dynamics. We show that over the first 5-years post-fire, fast-growing bacterial heterotrophs colonize regions of the soil previously occupied by slower-growing saprotrophic fungi. The bacterial heterotrophs mineralize organic matter, releasing nutrients into the soil. This pathway outweighs new sources of nitrogen and facilitates the recovery of plant productivity. We broadly show here that while consideration of distinct microbial metabolisms related to carbon and nutrient cycling remains rare in terrestrial ecosystem models, they are important when considering the rate of ecosystem recovery post-disturbance and the feedback to soil nutrient cycles on centennial timescales.

Inter-microbial competition for N and plant NO3− uptake rather than BNI determines soil net nitrification under intensively managed Brachiaria humidicola

Brachiaria humidicola (syn. Urochloa humidicola) has been acknowledged to control soil nitrification through release of nitrification inhibitors (NI), a phenomenon conceptualized as biological nitrification inhibition (BNI). Liming and N fertilization as features of agricultural intensification may suppress BNI performance, due to a decrease in NI exudation, increased NH3 availability and promotion of ammonia oxidizing bacteria (AOB) over archaea (AOA). A 2-year three-factorial pot trial was conducted to investigate the influence of soil pH and soil microbial background (ratio of archaea to bacteria) on BNI performance of B. humidicola. The study verified the capacity of B. humidicola to reduce net nitrification rates by 50 to 85% compared to the non-planted control, irrespective of soil pH and microbial background. The reduction of net nitrification, however, was largely dependent on microbial N immobilization and efficient plant N uptake. A reduction of gross nitrification could not be confirmed for the AOA dominated soil, but possibly contributed to reduced net nitrification rates in the AOB-dominated soil. However, this putative reduction of gross nitrification was attributed to plant-facilitated inter-microbial competition between bacterial heterotrophs and nitrifiers rather than BNI. It was concluded that BNI may play a dominant role in extensive B. humidicola pasture systems, while N immobilization and efficient plant N uptake may display the dominant factors controlling net nitrification rates under intensively managed B. humidicola.

Changing expression patterns of TonB-dependent transporters suggest shifts in polysaccharide consumption over the course of a spring phytoplankton bloom

Algal blooms produce large quantities of organic matter that is subsequently remineralised by bacterial heterotrophs. Polysaccharide is a primary component of algal biomass. It has been hypothesised that individual bacterial heterotrophic niches during algal blooms are in part determined by the available polysaccharide substrates present. Measurement of the expression of TonB-dependent transporters, often specific for polysaccharide uptake, might serve as a proxy for assessing bacterial polysaccharide consumption over time. To investigate this, we present here high-resolution metaproteomic and metagenomic datasets from bacterioplankton of the 2016 spring phytoplankton bloom at Helgoland island in the southern North Sea, and expression profiles of TonB-dependent transporters during the bloom, which demonstrate the importance of both the Gammaproteobacteria and the Bacteroidetes as degraders of algal polysaccharide. TonB-dependent transporters were the most highly expressed protein class, split approximately evenly between the Gammaproteobacteria and Bacteroidetes, and totalling on average 16.7% of all detected proteins during the bloom. About 93% of these were predicted to take up organic matter, and for about 12% of the TonB-dependent transporters, we predicted a specific target polysaccharide class. Most significantly, we observed a change in substrate specificities of the expressed transporters over time, which was not reflected in the corresponding metagenomic data. From this, we conclude that algal cell wall-related compounds containing fucose, mannose, and xylose were mostly utilised in later bloom stages, whereas glucose-based algal and bacterial storage molecules including laminarin, glycogen, and starch were used throughout. Quantification of transporters could therefore be key for understanding marine carbon cycling.

Resource partitioning of phytoplankton metabolites that support bacterial heterotrophy

The communities of bacteria that assemble around marine microphytoplankton are predictably dominated by Rhodobacterales, Flavobacteriales, and families within the Gammaproteobacteria. Yet whether this consistent ecological pattern reflects the result of resource-based niche partitioning or resource competition requires better knowledge of the metabolites linking microbial autotrophs and heterotrophs in the surface ocean. We characterized molecules targeted for uptake by three heterotrophic bacteria individually co-cultured with a marine diatom using two strategies that vetted the exometabolite pool for biological relevance by means of bacterial activity assays: expression of diagnostic genes and net drawdown of exometabolites, the latter detected with mass spectrometry and nuclear magnetic resonance using novel sample preparation approaches. Of the more than 36 organic molecules with evidence of bacterial uptake, 53% contained nitrogen (including nucleosides and amino acids), 11% were organic sulfur compounds (including dihydroxypropanesulfonate and dimethysulfoniopropionate), and 28% were components of polysaccharides (including chrysolaminarin, chitin, and alginate). Overlap in phytoplankton-derived metabolite use by bacteria in the absence of competition was low, and only guanosine, proline, and N-acetyl-d-glucosamine were predicted to be used by all three. Exometabolite uptake pattern points to a key role for ecological resource partitioning in the assembly marine bacterial communities transforming recent photosynthate.

Sulfur metabolites that facilitate oceanic phytoplankton-bacteria carbon flux.

Unlike biologically available nitrogen and phosphorus, which are often at limiting concentrations in surface seawater, sulfur in the form of sulfate is plentiful and not considered to constrain marine microbial activity. Nonetheless, in a model system in which a marine bacterium obtains all of its carbon from co-cultured phytoplankton, bacterial gene expression suggests that at least seven dissolved organic sulfur (DOS) metabolites support bacterial heterotrophy. These labile exometabolites of marine dinoflagellates and diatoms include taurine, N-acetyltaurine, isethionate, choline-O-sulfate, cysteate, 2,3-dihydroxypropane-1-sulfonate (DHPS), and dimethylsulfoniopropionate (DMSP). Leveraging from the compounds identified in this model system, we assessed the role of sulfur metabolites in the ocean carbon cycle by mining the Tara Oceans dataset for diagnostic genes. In the 1.4 million bacterial genome equivalents surveyed, estimates of the frequency of genomes harboring the capability for DOS metabolite utilization ranged broadly, from only 1 out of every 190 genomes (for the C2 sulfonate isethionate) to 1 out of every 5 (for the sulfonium compound DMSP). Bacteria able to participate in DOS transformations are dominated by Alphaproteobacteria in the surface ocean, but by SAR324, Acidimicrobiia, and Gammaproteobacteria at mesopelagic depths, where the capability for utilization occurs in higher frequency than in surface bacteria for more than half the sulfur metabolites. The discovery of an abundant and diverse suite of marine bacteria with the genetic capacity for DOS transformation argues for an important role for sulfur metabolites in the pelagic ocean carbon cycle.

Genomic reconstructions and potential metabolic strategies of generalist and specialist heterotrophic bacteria associated with an estuary Synechococcus culture.

Interactions between photoautotrophs and heterotrophs are central to marine microbial ecosystems. Synechococcus are dominant marine phototrophs, and they are frequently associated with heterotrophic bacteria. These co-cultures provide a useful research system to investigate photoautotroph-heterotroph interactions in marine systems. Bacteria within the Roseobacter clade and Flavobacteria are two of the main bacterial lineages that exhibit intimate associations with Synechococcus populations. We conducted metagenomic analyses of a Synechococcus culture, followed by genomic binning of metagenomic contigs, and recovered five nearly complete genomes, including members of the Roseobacter clade (i.e. Marivita sp. XM-24) and Flavobacteria (i.e. Fluviicola sp. XM-24). Marivita sp. XM-24 is an ecological generalist of the Roseobacter clade and displays diverse metabolic capacities for the acquisition of nutrients and energy sources. Specifically, the genome contained numerous gene complements involved in the uptake and metabolism of nitrogen- and phosphorus-containing inorganic and organic compounds, in addition to the potential for aerobic anoxygenic photosynthesis, oxidation of carbon monoxide, inorganic sulfur oxidation, DMSP demethylation and PHA metabolism. The genome of the Flavobacteria representative, Fluviicola sp. XM-24, contained numerous peptidases, glycoside hydrolases, adhesion-related proteins and genes involved in gliding motility. Fluviicola sp. XM-24 likely specialize in the degradation of high molecular weight compound exudates from Synechococcus cells, including polysaccharides and polypeptides via attachment to particles, surfaces or cells. The distinct metabolic strategies identified within several heterotrophic bacteria that are associated with Syneochococcus cells provide insights into their lifestyles and nutrient utilization patterns, in addition to their interactions with photoautotrophs. Biological interactions, including mutualism, competition and antagonism, shape the microbial community structure of marine environments and are critical for understanding biogeochemical cycling in the ocean. These results provide valuable insights into the nature of interactions between dominant marine photoautotrophs and associated bacterial heterotrophs.

Fungal\u2013bacterial dynamics and their contribution to terrigenous carbon turnover in relation to organic matter quality

Ecological functions of fungal and bacterial decomposers vary with environmental conditions. However, the response of these decomposers to particulate organic matter (POM) quality, which varies widely in aquatic ecosystems, remains poorly understood. Here we investigated how POM pools of substrates of different qualities determine the relative contributions of aquatic fungi and bacteria to terrigenous carbon (C) turnover. To this end, surface sediments were incubated with different POM pools of algae and/or leaf litter. 13C stable-isotope measurements of C mineralization were combined with phospholipid analysis to link the metabolic activities and substrate preferences of fungal and bacterial heterotrophs to dynamics in their abundance. We found that the presence of labile POM greatly affected the dominance of bacteria over fungi within the degrader communities and stimulated the decomposition of beech litter primarily through an increase in metabolic activity. Our data indicated that fungi primarily contribute to terrigenous C turnover by providing litter C for the microbial loop, whereas bacteria determine whether the supplied C substrate is assimilated into biomass or recycled back into the atmosphere in relation to phosphate availability. Thus, this study provides a better understanding of the role of fungi and bacteria in terrestrial–aquatic C cycling in relation to environmental conditions.

Saharan dust nutrients promote Vibrio bloom formation in marine surface waters

Vibrio is a ubiquitous genus of marine bacteria, typically comprising a small fraction of the total microbial community in surface waters, but capable of becoming a dominant taxon in response to poorly characterized factors. Iron (Fe), often restricted by limited bioavailability and low external supply, is an essential micronutrient that can limit Vibrio growth. Vibrio species have robust metabolic capabilities and an array of Fe-acquisition mechanisms, and are able to respond rapidly to nutrient influx, yet Vibrio response to environmental pulses of Fe remains uncharacterized. Here we examined the population growth of Vibrio after natural and simulated pulses of atmospherically transported Saharan dust, an important and episodic source of Fe to tropical marine waters. As a model for opportunistic bacterial heterotrophs, we demonstrated that Vibrio proliferate in response to a broad range of dust-Fe additions at rapid timescales. Within 24 h of exposure, strains of Vibrio cholerae and Vibrio alginolyticus were able to directly use Saharan dust-Fe to support rapid growth. These findings were also confirmed with in situ field studies; arrival of Saharan dust in the Caribbean and subtropical Atlantic coincided with high levels of dissolved Fe, followed by up to a 30-fold increase of culturable Vibrio over background levels within 24 h. The relative abundance of Vibrio increased from ∼1 to ∼20% of the total microbial community. This study, to our knowledge, is the first to describe Vibrio response to Saharan dust nutrients, having implications at the intersection of marine ecology, Fe biogeochemistry, and both human and environmental health.

Pelagic microbial heterotrophy in response to a highly productive bloom of Phaeocystis antarctica in the Amundsen Sea Polynya, Antarctica

Abstract Heterotrophic bacteria play a key role in marine carbon cycling, and understanding their activities in polar systems is important for considering climate change impacts there. One goal of the ASPIRE project was to examine the relationship between the phytoplankton bloom and bacterial heterotrophy in the Amundsen Sea Polynya (ASP). Bacterial abundance, production (BP), respiration, growth efficiency, and extracellular enzyme activity (EEA) were compared to nutrient and organic matter inventories, chlorophyll a (Chl a), viral and microzooplankton abundance, and net primary production (NPP). Bacterial production and respiration clearly responded (0.04–4.0 and 10–53 µg C L−1 d−1, respectively) to the buildup of a massive Phaeocystis antarctica bloom (Chl a: 0.2–22 µg L−1), with highest rates observed in the central polynya where Chl a and particulate organic carbon (POC) were greatest. The highest BP rates exceeded those reported for the Ross Sea or any other Antarctic coastal system, yet the BP:NPP ratio (2.1–9.4%) was relatively low. Bacterial respiration was also high, and growth efficiency (2–27%; median = 10%) was similar to oligotrophic systems. Thus, the integrated bacterial carbon demand (0.8–2.8 g C m−2 d−1) was a high fraction (25–128%; median = 43%) of NPP during bloom development. During peak bloom, activity was particle-associated: BP and EEA correlated well with POC, and size fractionation experiments showed that the larger size fraction (&amp;gt; 3 µm) accounted for a majority (∼ 75%) of the BP. The community was psychrophilic, with a 5x reduction in BP when warmed to 20°C. In deeper waters, respiration remained relatively high, likely fueled by the significant downward particle flux in the region. A highly active, particle-associated, heterotrophic microbial community clearly responded to the extraordinary phytoplankton bloom in the ASP, likely limiting biological pump efficiency during the early season.

Effects of hydrocarbon contamination on soil microbial community and enzyme activity

Soil enzymatic activities and microbial biomass carbon (Cmic) are considered to be two important soil biological activities influenced by oil contamination occurring in the soil ecosystem. This study focused on changes in the soil microbial community enzymatic activities as a result of the potential inhibitory effects of hydrocarbon contamination. The relationship between hydrocarbons (kerosene and diesel), Cmic and enzymatic activity (dehydrogenase and phosphatase) was evaluated in three amended soil types collected from different areas (Fresh Boyndie, Insch and Brechin) in Aberdeenshire (UK). Results showed that hydrocarbon contamination inhibited enzymatic activities in all the amended soil samples. The extent of inhibition increased significantly with increasing levels of hydrocarbons, and varied with the incubation period. Insch soil had high Cmic values and high numbers of heterotrophic bacteria CFU, but it had the lowest dehydrogenase and phosphatase activities of all three soils. Brechin soils had the highest phosphatase activity. Results also showed that both Insch and Brechin soils had similar numbers of culturable hydrocarbon degrader bacteria across all soil treatments with the exception of kerosene treatments, while Brechin soils had the highest culturable numbers of hydrocarbon degrading fungi across all three soil treatments with the exception of incubated control and kerosene treatments. There were generally strong positive relationships in non-treated samples between bacterial heterotrophs and hydrocarbon degrading bacteria in all three soils. Both incubated Insch and Brechin soil treatments exhibited a strong correlation between fungal heterotrophs and hydrocarbon degraders. However, non-incubated Insch and Brechin soils had a weak relationship between fungal heterotrophs and degrading fungi. Hydrocarbons in soils provide a source of carbon for microbial growth and this helps to explain the high variation in fungal data between soils which may be associated with different microbial communities in each soil.

Lipid and 13C signatures of submicron and suspended particulate organic matter in the Eastern Tropical North Pacific: Implications for the contribution of Bacteria

The contribution of bacterial biomass to total particulate organic matter (POM) in the ocean, including exported material, is poorly constrained. To examine potential signatures for the presence and export of bacterioplankton and their detrital remains, here we provide a detailed compound-specific 13C characterization of fatty acids from membrane polar lipids obtained from a water column profile in the Eastern Tropical North Pacific. POM of submicron size (0.2–0.7μm; “X-POM”) was sampled and analyzed separately from the size class typically collected as “suspended” POM (0.7–53μm; “L-POM”). The distributions of polar head group classes, specific fatty acid side chains, and natural 13C contents all vary, both between particle size classes and with depth in the water column. In general, the polar lipids in submicron material – and by inference, lipids of bacterial origin – have higher 13C content than polar lipids from larger POM and are equally abundant. Lipid signatures from the photic zone appear to be partially conserved in the suspended pool during transit down the water column. However, bacterial heterotrophy and possibly chemoautotrophy partially overprint these surface signatures. In addition, active metabolisms in the oxygen minimum zone (OMZ) appear to mediate the disaggregation of POM transported from the surface, thus adding complexity to the pathways of mid-water carbon flux and providing additional organic substrates to the OMZ and below. This “substrate injection” may provide important fuel for the denitrification and anammox reactions. Finally, examination of 13C content in polar lipids provides a basis for new interpretation of depth-related variations in δ13C values of bulk suspended POM.

Fungi mediate nitrous oxide production but not ammonia oxidation in aridland soils of the southwestern US

Nitrification and denitrification are key processes that control nitrogen (N) availability and loss in terrestrial systems. Nitrification in soils is thought to be performed primarily by chemoautotrophic prokaryotes such as bacteria and archaea, and denitrification by bacterial heterotrophs. However, recent work in drylands suggests that fungi may play a larger role in N transformations than previously recognized. Arid and semi-arid ecosystems experience extreme temperatures and low moisture conditions, both of which favor growth and survival of some fungi, but the extent of fungal nitrification and denitrification in these soils has not been explored. We investigated the role of fungi in nitrate (NO3−) and nitrous oxide (N2O) production in soils from regions across the southwestern US. Soils were collected from urban and Sonoran Desert sites within the Phoenix metropolitan area in Arizona, and from grasslands in Arizona and New Mexico. Rates of potential nitrification were measured in soils subjected to biocide treatments (fungal and bacterial inhibitors) and acetylene, an inhibitor of autotrophic ammonia oxidation. Nitrous oxide production was measured from soils incubated at two moisture levels in the presence of the biocide treatments. Rates of potential nitrification decreased significantly in all soils with additions of acetylene, indicating that autotrophic microorganisms may dominate ammonia oxidation and NO3− production rather than heterotrophs (e.g., fungi). Similarly, fungi played a minor role in N2O production in urban turfgrass soils that were highly managed with irrigation and fertilizers. In contrast, fungi were major sources of N2O production in desert and semi-arid grassland soils across a range of soil water content. We conclude that fungi are likely responsible for denitrification in aridland soils, and that land-use changes associated with urbanization alter the biotic pathways responsible for N cycling.

Sticking properties of transparent exopolymeric particles (TEP) during aging and biodegradation

Although many studies have addressed the role of bacteria in the degradation of organic matter, few have examined how bacteria alter the physicochemical properties of dissolved and colloidal organic matter in coastal systems. Here, we investigate how the sticking properties of transparent exopolymeric particles (TEP) varied with DOM age in batch cultures. We show that in two contrasted sites, despite different initial TEP sticking properties and bulk concentrations, after 48 h, the sticking properties were similar and increased (i.e. TEP became stickier) with increasing DOM age. We propose that TEP occurring after 48 h of incubation are mainly of heterotrophic origin, which is in contrast to the previously identified TEP of autotrophic origin. These results highlight the potential importance of bacterial DOM production, particularly in the aphotic zone, and further underline the potential of bacterial heterotrophs to produce biologically refractory dissolved organic matter that is physically reactive (i.e. sticky).

Availability of glucose and light modulates the structure and function of a microbial biofilm

We have studied the differences in the organic matter processing and biofilm composition and structure between autoheterotrophic and heterotrophic biofilm communities. Microbial communities grown on artificial biofilms were monitored, following incubation under light and dark conditions and with or without the addition of glucose as a labile organic compound. Glucose addition greatly affected the microbial biofilm composition as shown by differences in 16S rRNA gene fingerprints. A significant increase in beta-glucosidase and peptidase enzyme activities were also observed in glucose-amended biofilms incubated in the dark, suggesting an active bacterial community. Light enhanced the algal and bacterial growth, as well as higher extracellular enzyme activity, thereby indicating a tight algal-bacterial coupling in biofilms incubated under illumination. In these biofilms, organic compounds excreted by photosynthetic microorganisms were readily available for bacterial heterotrophs. This algal-bacterial relationship weakened in glucose-amended biofilms grown in the light, probably because heterotrophic bacteria preferentially use external labile compounds. These results suggest that the availability of labile organic matter in the flowing water and the presence of light may alter the biofilm composition and function, therefore affecting the processing capacity of organic matter in the stream ecosystem.

Spatiotemporal Variation of Bacterial Assemblages in a Shallow Subtropical Coastal Lagoon in Southern Brazil

A study on the bacterioplankton of Conceição Lagoon (27 degrees 34' S-48 degrees 27' W), Southern Brazil, was carried out in July 2005 (austral winter) and January 2006 (austral summer) to characterize the bacterial spatiotemporal distribution and to determine the heterotrophic and photoautotrophic bacterial dominance in hypoxic/oxic stratified waters. Bacterial abundance increased significantly (p < 0.05) in summer with averages of coccus cyanobacteria (CCY) ranging from 1.02 x 10(5) (winter) to 3.21 x 10(6) cells mL(-1) (summer), heterotrophic coccus/rod-shaped (HCR) cells from 7.00 x 10(4) to 3.60 x 10(6) cells mL(-1), and heterotrophic filamentous (HF) bacteria from 2.90 x 10(3) to 2.74 x 10(5) cells mL(-1). Bacterial biovolumes also increased in summer with mean biovolumes of CCY ranging from 0.38 to 1.37 microm3, HCR cells from 0.31 to 1.12 microm3, and HF from 3.32 to 11.34 microm3. Principal component analysis showed that salinity, temperature, and light were the abiotic factors that better explained the temporal variability of bacterial assemblages. Bacterial heterotrophy dominated in the lagoon, excepted by the southern and part of central sector in January 2006, when autotrophic-dominated microbial community occurred. Spatially, bacterial assemblages were influenced by nutrient gradient, oxygen, and salinity with a positive relationship between biovolumes and nutrients and a negative relationship between abundance of coccus cyanobacteria and nutrients. The stratified [corrected] area revealed a singular temporal pattern with hypoxic bottom waters in winter and oxygen-rich waters appearing in summer related with the availability of light and predominant microbes. Thus, oxygen consumption/production is likely to be regulated by the amount of light reaching the bottom, stimulating the production of oxygen by oxygenic phototrophs.