Silvio Pantoja

Sulfate reduction and methanogenesis in a Thioploca-dominated sediment off the coast of Chile

Continental shelf sediments of the central Chile upwelling area are dominated by the presence of dense mats of the filamentous, sulfur-depositing bacterium Thioploca spp. We examined rates and pathways of S and methane cycling in these sediments along a transect from the Bay of Concepcion to the continental slope. Sulfate reduction rates (170–4670 nmol cm−3 d−1) were equal to or exceeded rates reported for other subtidal marine sediments. Elemental S and pyrite were the dominant end-products of sulfate reduction in Thioploca mats on the continental shelf, whereas, in the highly-reducing, Beggiatoa-dominated sediments of the nearby Bay of Concepcion, acid-volatile S was the principal end-product. Dissolved organic C values were lowest at the stations with the highest sulfate reduction rates and increased offshore. Sediment porewater methane concentrations in all surface sediments were low (<12 nmol cm−3), and methane production rates at the station most dominated by Thioploca were extremely low ( <0.5 nmol cm−3 d−1). Low methane production rates and concentrations were matched by low methane oxidation rates (<0.1 nmol cm−3 d−1). Radio-tracer studies showed that methane production was almost exclusively from methylamines, substrates which are noncompetitive with sulfate reduction, rather than from acetate or CO2/H2. Bacterial MPN (most probable number) counts also indicated the presence of a methylotrophic population of methanogens. Surprisingly, high numbers of autotrophic acetogenic bacteria were found, suggesting that the bacterial population involved in anaerobic DOC degradation is more complex than expected. In spite of the high sulfate reduction rates, sulfide concentrations in the shelf and slope were low or undetectable (<0.5 μM), and sulfate concentrations were never depleted below bottom water levels down to depths of 25–30 cm. Calculations suggest that Thioploca were oxidizing a maximum of 35% of sulfide production—not enough to prevent sulfate depletion. Either other sulfide oxidizers were also present or transient hydrodynamic conditions coupled with bioturbation resulted in oxidation of the sediments.

Stable isotope constraints on the nitrogen cycle of the Mediterranean Sea water column

We usedthe nitrogen isotope ratio of algae, suspend edparticles andnitrate in the water column to track spatial variations in the marine nitrogen cycle in the Mediterranean Sea. Surface PON (5–74 m) was more depleted in 15 Ni n the eastern basin (� 0.370.5%) than in the western basin (+2.471.4%), suggesting that nitrogen suppliedby biological N 2 fixation may be an important source of new nitrogen in the eastern basin, where preformednitrate from the Atlantic Ocean could have been depleted during its transit eastward. The d 15 N of nitrate in the deep Mediterranean (B3% in the western-most Mediterranean and decreasing toward the east) is significantly lower than nitrate at similar depths from the North Atlantic (4.8–5%), also suggesting an important role for N2 fixation. The eastwardd ecrease in the d 15 No f surface PON is greater than the eastwarddecrease in the d 15 N of the subsurface nitrate, implying that the amount of N2 fixation in the eastern Mediterranean is great enough to cause a major divergence in the d 15 N of phytoplankton biomass from the d 15 N of the nitrate upwelledfrom below. Variations in prod uctivity associatedwith frontal processes, including shoaling of the nitracline, did not lead to detectable variations in the d 15 N of PON. This indicates that no differential fertilization or productivity gradient occurred in the Almerian/Oran area. Our results are consistent with a lack of gradient in chlorophyll-a (chl-a) andnitrate concentration in the Alboran Sea. 15 N enrichment in particles below 500 m depth was detected in the Alboran Sea with respect to surface PON, reaching an average value of +7.470.7%. The d 15 N in sinking particles caught at 100 m depth (4.9–5.6%) was intermediate between suspended surface and suspended deep particles. We found a consistent difference in the isotopic composition of nitrogen in PON compared with that of chlorophyll (Dd 15 N[PON-chlorin]=+6.471.4%) in the surface, similar to the offset reportedearlier in cultures for cellular N andchl- a. This indicates that d 15 N of phytoplankton biomass was retainedin surface PON, and that alteration of the isotopic signal of PON at depth was due to heterotrophic activity. r 2002 Elsevier Science Ltd. All rights reserved.

Hydrolysis of peptides in seawater and sediment

Abstract Protein hydrolysis and subsequent peptide production appear to be the links between degradation of protein and production of free amino acids in the marine environment. This model has not yet been fully demonstrated because neither presence of peptides nor peptide hydrolysis has been directly measured in seawater or sediments. Fluorescent Lucifer Yellow (LYA)-derivatives of several peptides were synthesized and tested for use as models in an investigation of peptide hydrolysis in seawater and sediment. We demonstrated that these LYA-derivatives behave to some degree as the natural peptides by showing that LYA-dialanine effectively competes with dialanine (ala 2 ) for the active sites of microbial hydrolytic enzymes found in seawater. LYA-derivatives of ala 2 , ala-leu and ala 4 hydrolyzed to smaller peptides or free amino acids in both seawater and sediments. In seawater, hydrolysis of the longer peptide, LYA-ala 4 was 90 × faster than hydrolysis of LYA-ala 2 and 30 × faster than LYA-ala-leu. In sediments, rapid disappearance of the initially-added substrate LYA-ala 4 from pore waters was followed by slower production of LYA-ala 3 , LYA-ala 2 and LYA-ala. Hydrolysis was not random; preferential cleavage of certain peptide bonds occurred.

Peptide decomposition by extracellular hydrolysis in coastal seawater and salt marsh sediment

Abstract Extracellular peptide hydrolysis rates were measured in seawater and sediment from Flax Pond salt marsh using peptide analogs (LYA-peptides) as substrates. This technique allows the direct measurement of specific hydrolysis products and thus provides insights into enzymatic hydrolysis pathways. In sediments, hydrolysis rate constants of LYA-peptides varied seasonally and with depth. Highest activity was found in spring and summer, and most cores exhibited a subsurface maximum. Calculations using the concentrations of chemically-measured peptides suggested that extracellular hydrolysis of peptides is faster than the rate of free amino acids uptake. However, not all peptides may be available for enzymatic hydrolysis. In both seawater and sediment, extracellular hydrolysis of peptides of up to 8 amino acids yielded smaller peptides and free amino acids. Hydrolysis rates depended on size of the peptide substrate, although a clear relationship with number of amino acid constituents was not evident. Peptides containing >2 amino acids were hydrolyzed 10–400 times faster than dipeptides or the fluorogenic substrate Leucine-MCA. Thus, dipeptidases are either uncommon in nature, or hydrolysis is carried out by nonspecific hydrolases that with a low affinity for dipeptides. This is also suggested by the presence of a lag time before dipeptide hydrolysis begins, and the absence of dipeptide hydrolysis in 0.2-μm-filtered. One implication of this finding is that measurements of hydrolysis rates using substrates like Leu-MCA may not accurately predict the magnitude of hydrolysis rates of macromolecules in the marine environment. Even though dipeptide hydrolysis is slow compared to that of larger peptides, LYA-dipeptides are preferentially produced from the hydrolysis of larger substrates. LYA-dipeptides do not penetrate cell membranes of microorganisms because of their size, but natural dipeptides are smaller and can be transported across the cell membrane. Since dipeptides do not appear to accumulate in natural waters, they must be rapidly removed by microorganisms.

A single-cell sequencing approach to the classification of large, vacuolated sulfur bacteria

The colorless, large sulfur bacteria are well known because of their intriguing appearance, size and abundance in sulfidic settings. Since their discovery in 1803 these bacteria have been classified according to their conspicuous morphology. However, in microbiology the use of morphological criteria alone to predict phylogenetic relatedness has frequently proven to be misleading. Recent sequencing of a number of 16S rRNA genes of large sulfur bacteria revealed frequent inconsistencies between the morphologically determined taxonomy of genera and the genetically derived classification. Nevertheless, newly described bacteria were classified based on their morphological properties, leading to polyphyletic taxa. We performed sequencing of 16S rRNA genes and internal transcribed spacer (ITS) regions, together with detailed morphological analysis of hand-picked individuals of novel non-filamentous as well as known filamentous large sulfur bacteria, including the hitherto only partially sequenced species Thiomargarita namibiensis, Thioploca araucae and Thioploca chileae. Based on 128 nearly full-length 16S rRNA-ITS sequences, we propose the retention of the family Beggiatoaceae for the genera closely related to Beggiatoa, as opposed to the recently suggested fusion of all colorless sulfur bacteria into one family, the Thiotrichaceae. Furthermore, we propose the addition of nine Candidatus species along with seven new Candidatus genera to the family Beggiatoaceae. The extended family Beggiatoaceae thus remains monophyletic and is phylogenetically clearly separated from other related families.

Fluctuaciones en la abundancia de microorganismos silíceos preservados en los sedimentos del canal Puyuhuapi (44° S), Chile, durante el siglo XX

Se presenta una reconstruccion de 100 anos de la productividad silicea exportada en sedimentos del canal Puyuhuapi (44° S, 70° O) en los fiordos chilenos. Se utilizan las tasas de acumulacion y las concentraciones de diatomeas y silicoflagelados, carbono organico (Corg) y silice biogenico (SiOPAL) como indicadores de la produccion exportada y las fluctuaciones en la contribucion de diatomeas de agua dulce como indicadores de precipitacion y descargas de rios. Se analizaron muestras de sedimentos colectadas mediante un sacatestigo de caja en dos sitios en el canal Puyuhuapi: Estacion 35 (ubicada en la cabeza del fiordo dentro del seno Ventisquero; 56 m de profundidad) y Estacion 40 (en la mitad del canal; 270 m de profundidad de agua). Las tasas de sedimentacion superficial fueron de 0,75 cm ano-1 en la Estacion 35 y 0,25 cm ano-1 en la Estacion 40. En ambos sitios el contenido promedio de SiOPAL fue de ~ 4 %. Las tasas de acumulacion de diatomeas asi como la contribucion de diatomeas de agua dulce fueron mas altas en la cabeza del fiordo (1,59 1010 valvas m-2 ano-1 y 22 %) que en la mitad de este (1,08 1010 valvas m-2 ano-1 y 14 % respectivamente). Las abundancias de diatomeas fueron dos ordenes de magnitud mas altas que la contribucion de silicoflagelados. En general, los sedimentos del canal Puyuhuapi son caracterizados por diatomeas tipicas de ambientes de altos nutrientes: en ambos sitios, las esporas del genero Chaetoceros dominan la asociacion de diatomeas (> 40 % de la asociacion total de diatomeas, esporas de Chaetoceros radicans/cinctus, Ch. constrictus/vanheurcki, Ch. debilis y Ch. diadema). En general se observa un aumento en la tasa de acumulacion de microorganismos siliceos desde finales del siglo XIX hasta comienzos de 1980, y un descenso hacia finales de la decada de 1990. Asociamos una disminucion en la diatomeas, silice biogenico y silicoflagelados hacia el presente, sugiriendo una reduccion en la productividad. Esto es acompanado por una disminucion en las diatomeas de agua dulce desde mediados de los anos 1970, con una disminucion concomitante en la precipitacion en el area de los fiordos chilenos. Sugerimos que dicha disminucion se relaciona con el calentamiento atmosferico y oceanico global de los ultimos 25 anos

Assessing the micro-phytoplankton response to nitrate in Comau Fjord (42°S) in Patagonia (Chile), using a microcosms approach

Anthropogenic (aquaculture) changes in environment nutrient concentrations may affect phytoplankton (biomass and taxa composition) in marine coastal waters off the Chilean Patagonia. The effects of adding nitrate (NO3−) to natural phytoplankton assemblages were evaluated considering biomass, cell abundance, and taxonomic composition. Microcosm experiments were performed in the spring, summer, and winter in the Comau Fjord located in Subantarctic Patagonia. At the end of the experiments, NO3− decreased rapidly and was undetectable in treatments, indicating a strong NO3− deficiency associated with an exponential increase in Chl-a concentrations, particulate organic nitrogen, and carbon in these treatments. Moreover, given the depleted nitrate concentrations of the spring and summer experiments, the micro-phytoplankton taxa structure shifted from mixed diatom and dinoflagellate assemblages (Ceratium spp., Dinophysis spp., Coscinodiscus sp., Rhizosolenia pungens) to assemblages dominated by blooms of the classic chain-forming diatoms found in temperate and cold waters such as Chaetoceros spp., Skeletonema spp., and Thalassiosira spp. Thus, nitrogen sources (i.e., nitrate, ammonia) may influence phytoplankton abundance and biomass accumulation dynamics in the northern section of Patagonia. It also emphasizes the importance of diatom taxa in regards to the short-term response of phytoplankton to changing environmental nutrient conditions due to natural (decreasing freshwater stream flow) and anthropogenic (aquaculture) events. This situation may be one of the future scenarios in the Patagonian fjords, thus stressing the needs for active environmental monitoring and impact assessment.

Hypoxia causes preservation of labile organic matter and changes seafloor microbial community composition (Black Sea)

Hypoxia enhances organic matter preservation in marine sediments by changing benthic communities, bioturbation, and burial rates. Bottom-water oxygen supply is a key factor governing the biogeochemistry and community composition of marine sediments. Whether it also determines carbon burial rates remains controversial. We investigated the effect of varying oxygen concentrations (170 to 0 μM O2) on microbial remineralization of organic matter in seafloor sediments and on community diversity of the northwestern Crimean shelf break. This study shows that 50% more organic matter is preserved in surface sediments exposed to hypoxia compared to oxic bottom waters. Hypoxic conditions inhibit bioturbation and decreased remineralization rates even within short periods of a few days. These conditions led to the accumulation of threefold more phytodetritus pigments within 40 years compared to the oxic zone. Bacterial community structure also differed between oxic, hypoxic, and anoxic zones. Functional groups relevant in the degradation of particulate organic matter, such as Flavobacteriia, Gammaproteobacteria, and Deltaproteobacteria, changed with decreasing oxygenation, and the microbial community of the hypoxic zone took longer to degrade similar amounts of deposited reactive matter. We conclude that hypoxic bottom-water conditions—even on short time scales—substantially increase the preservation potential of organic matter because of the negative effects on benthic fauna and particle mixing and by favoring anaerobic processes, including sulfurization of matter.

Melting glacier impacts community structure of Bacteria, Archaea and Fungi in a Chilean Patagonia fjord

Jorge Montt glacier, located in the Patagonian Ice Fields, has undergone an unprecedented retreat during the past century. To study the impact of the meltwater discharge on the microbial community of the downstream fjord, we targeted Bacteria, Archaea and Fungi communities during austral autumn and winter. Our results showed a singular microbial community present in cold and low salinity surface waters during autumn, when a thicker meltwater layer was observed. Meltwater bacterial sequences were related to Cyanobacteria, Proteobacteria, Actinobacteria and Bacteriodetes previously identified in freshwater and cold ecosystems, suggesting the occurrence of microorganisms adapted to live in the extreme conditions of meltwater. For Fungi, representative sequences related to terrestrial and airborne fungal taxa indicated transport of allochthonous Fungi by the meltwater discharge. In contrast, bottom fjord waters from autumn and winter showed representative Operational Taxonomic Units (OTUs) related to sequences of marine microorganisms, which is consistent with current models of fjord circulation. We conclude that meltwater can significantly modify the structure of microbial communities and support the development of a major fraction of microorganisms in surface waters of Patagonian fjords.

First record of flamentous fungi in the coastal upwelling ecosystem off central Chile

Este estudio reporta por primera vez la presencia de hongos flamentosos en la columna de agua y sedimentos del ecosistema de surgencia costero de Chile central. La deteccion de hongos fue realizada utilizando herramientas moleculares y microscopia de epifuorescencia. Productos de amplifcacion positivos del gen 18s rADN fueron obtenidos para muestras de agua y sedimento superfcial de este ecosistema costero. El analisis de riqueza molecular de los productos de PCR, realizado por electroforesis en gel con gradiente denaturante, mostro un mayor numero de genotipos de hongos en las estaciones mas cercanas a la costa y durante el verano. Estructuras de hongos fueron identifcadas por microscopia de epifuorescencia y fueron observadas como flamentos individuales o como agregados de hifas. Nuestros resultados muestran los primeros perfles verticales de biomasa de hongos en el ecosistema marino. La biomasa de hongos alcanzo valores de hasta 5 µg C L-1 en aguas superfciales durante el verano y su estructura vertical fue similar a la observada para clorofla-a y consistente con la distribucion vertical general descrita para la biomasa microplactonica en el oceano. La presencia de hongos viables en el oceano costero plantea la necesidad de descifrar su rol en el procesamiento materia organica y evaluar su incorporacion en el paradigma actual del anillo microbiano y en los ciclos biogeoquimicos del oceano.