Viral community analysis in a marine oxygen minimum zone indicates increased potential for viral manipulation of microbial physiological state

AbstractMicrobial communities in oxygen minimum zones (OMZs) are known to have significant impacts on global biogeochemical cycles, but viral influence on microbial processes in these regions are much less studied. Here we provide baseline ecological patterns using microscopy and viral metagenomics from the Eastern Tropical North Pacific (ETNP) OMZ region that enhance our understanding of viruses in these climate-critical systems. While extracellular viral abundance decreased below the oxycline, viral diversity and lytic infection frequency remained high within the OMZ, demonstrating that viral influences on microbial communities were still substantial without the detectable presence of oxygen. Viral community composition was strongly related to oxygen concentration, with viral populations in low-oxygen portions of the water column being distinct from their surface layer counterparts. However, this divergence was not accompanied by the expected differences in viral-encoded auxiliary metabolic genes (AMGs) relating to nitrogen and sulfur metabolisms that are known to be performed by microbial communities in these low-oxygen and anoxic regions. Instead, several abundant AMGs were identified in the oxycline and OMZ that may modulate host responses to low-oxygen stress. We hypothesize that this is due to selection for viral-encoded genes that influence host survivability rather than modulating host metabolic reactions within the ETNP OMZ. Together, this study shows that viruses are not only diverse throughout the water column in the ETNP, including the OMZ, but their infection of microorganisms has the potential to alter host physiological state within these biogeochemically important regions of the ocean.

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Grapevine Phyllosphere Community Analysis in Response to Elicitor Application against Powdery Mildew

Microorganisms ◽

10.3390/microorganisms7120662 ◽

2019 ◽

Vol 7 (12) ◽

pp. 662 ◽

Cited By ~ 2

Author(s):

Luca Nerva ◽

Chiara Pagliarani ◽

Massimo Pugliese ◽

Matteo Monchiero ◽

Solène Gonthier ◽

...

Keyword(s):

Powdery Mildew ◽

Microbial Communities ◽

Defense Mechanisms ◽

High Throughput Sequencing ◽

Specific Activity ◽

Its Region ◽

Community Analysis ◽

Its Sequencing ◽

Viral Community ◽

Antimicrobial Treatments

The reduction of antimicrobial treatments and mainly the application of environmentally friendly compounds, such as resistance elicitors, is an impelling challenge to undertake more sustainable agriculture. We performed this research to study the effectiveness of non-conventional compounds in reducing leaf fungal attack and to investigate whether they influence the grape phyllosphere. Pathogenicity tests were conducted on potted Vitis vinifera “Nebbiolo” and “Moscato” cultivars infected with the powdery mildew agent (Erysiphe necator) and treated with three elicitors. Differences in the foliar microbial community were then evaluated by community-level physiological profiling by using BiologTM EcoPlates, high throughput sequencing of the Internal Transcribed Spacer (ITS) region, and RNA sequencing for the viral community. In both cultivars, all products were effective as they significantly reduced pathogen development. EcoPlate analysis and ITS sequencing showed that the microbial communities were not influenced by the alternative compound application, confirming their specific activity as plant defense elicitors. Nevertheless, “Moscato” plants were less susceptible to the disease and presented different phyllosphere composition, resulting in a richer viral community, when compared with the “Nebbiolo” plants. The observed effect on microbial communities pointed to the existence of distinct genotype-specific defense mechanisms independently of the elicitor application.

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Aura-biomes are present in the water layer above coral reef benthic macro-organisms

PeerJ ◽

10.7717/peerj.3666 ◽

2017 ◽

Vol 5 ◽

pp. e3666 ◽

Cited By ~ 8

Author(s):

Kevin Walsh ◽

J. Matthew Haggerty ◽

Michael P. Doane ◽

John J. Hansen ◽

Megan M. Morris ◽

...

Keyword(s):

Coral Reef ◽

Microbial Communities ◽

Water Column ◽

Coral Cover ◽

Coral Disease ◽

Benthic Organism ◽

Low Oxygen ◽

Surrounding Water ◽

Stressful Environment ◽

Turf Algae

As coral reef habitats decline worldwide, some reefs are transitioning from coral- to algal-dominated benthos with the exact cause for this shift remaining elusive. Increases in the abundance of microbes in the water column has been correlated with an increase in coral disease and reduction in coral cover. Here we investigated how multiple reef organisms influence microbial communities in the surrounding water column. Our study consisted of a field assessment of microbial communities above replicate patches dominated by a single macro-organism. Metagenomes were constructed from 20 L of water above distinct macro-organisms, including (1) the coral Mussismilia braziliensis, (2) fleshy macroalgae (Stypopodium, Dictota and Canistrocarpus), (3) turf algae, and (4) the zoanthid Palythoa caribaeorum and were compared to the water microbes collected 3 m above the reef. Microbial genera and functional potential were annotated using MG-RAST and showed that the dominant benthic macro-organisms influence the taxa and functions of microbes in the water column surrounding them, developing a specific “aura-biome”. The coral aura-biome reflected the open water column, and was associated with Synechococcus and functions suggesting oligotrophic growth, while the fleshy macroalgae aura-biome was associated with Ruegeria, Pseudomonas, and microbial functions suggesting low oxygen conditions. The turf algae aura-biome was associated with Vibrio, Flavobacterium, and functions suggesting pathogenic activity, while zoanthids were associated with Alteromonas and functions suggesting a stressful environment. Because each benthic organism has a distinct aura-biome, a change in benthic cover will change the microbial community of the water, which may lead to either the stimulation or suppression of the recruitment of benthic organisms.

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Life at stable low oxygen levels: adaptations of animals to oceanic oxygen minimum layers.

Journal of Experimental Biology ◽

10.1242/jeb.201.8.1223 ◽

1998 ◽

Vol 201 (8) ◽

pp. 1223-1232 ◽

Cited By ~ 15

Author(s):

J J Childress ◽

B A Seibel

Keyword(s):

Water Column ◽

Aerobic Metabolism ◽

Oxygen Level ◽

Low Oxygen ◽

Oxygen Levels ◽

Surface Areas ◽

Partial Pressures ◽

Stable Conditions ◽

Consumption Rates ◽

Oxygen Minimum

Zones of minimum oxygen level are found at intermediate depths in most of the world's oceans and, although the oxygen partial pressure in some of these 'oxygen minimum layers' is only a fraction of a kilopascal, populations of pelagic metazoans exist there. These oxygen minimum layers are areas of the water column and the associated benthos with stable conditions of continuously low oxygen level and low temperature at intermediate depths (400-1000 m depth) over vast areas. Off California, where PO2 at the oxygen minimum is 0.8 kPa, there are abundant populations of animals both in the water column and on the bottom. Farther to the south in the eastern tropical Pacific, oxygen partial pressures of less than approximately 0.4 kPa result in very low biomasses and diversity of animals at minimum layer depths. At the minimum oxygen levels found off California, most animals which inhabit the minimum zones appear to support their routine metabolic demands via aerobic metabolism. They do this by being very effective at removing oxygen from water. Among the adaptations of pelagic crustaceans to these conditions are: (1) enhanced ventilatory abilities, (2) enhanced percentage removal of O2 from the ventilatory stream, (3) large gill surface areas, (4) short diffusion distances from the water to the blood, and (5) hemocyanin respiratory proteins with a very high affinity for O2, high cooperativity and large Bohr effects. The lower O2 consumption rates of many deeper-living species are also functionally adaptive in that they facilitate aerobic survival at low PO2. However, they are not adaptations to the minimum layer, since similarly low rates are found in the same and comparable species living at the same depths in regions without well-developed minima, and these animals are unable to survive at the low PO2 values of the minima. While anaerobic metabolism may be important for metabolic rates above the routine level for most animals in the minimum layer, there is little evidence for the use of sustained anaerobiosis in the species studied. In summary, given the stable presence of very low O2 levels in the minima, the primary adaptations of animals living within them are those that support aerobic metabolism by giving the animals remarkable abilities to extract O2 from water. These abilities are notably better than those of animals adapted to unstable hypoxic environments, such as intertidal mudflats, while the latter animals rely to a much greater extent on anaerobiosis and perhaps on metabolic suppression to survive periods of anoxia.

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Differential Distribution and Determinants of Ammonia Oxidizing Archaea Sublineages in the Oxygen Minimum Zone off Costa Rica

Microorganisms ◽

10.3390/microorganisms7100453 ◽

2019 ◽

Vol 7 (10) ◽

pp. 453 ◽

Cited By ~ 1

Author(s):

Yanhong Lu ◽

Xiaomin Xia ◽

Shunyan Cheung ◽

Hongmei Jing ◽

Hongbin Liu

Keyword(s):

Costa Rica ◽

Water Column ◽

Gulf Of California ◽

North Pacific Ocean ◽

Oxygen Minimum Zone ◽

Low Oxygen ◽

Environmental Determinants ◽

Ammonia Oxidizing Archaea ◽

Minimum Zone ◽

Oxygen Minimum

Ammonia oxidizing archaea (AOA) are microbes that are widely distributed in the ocean that convert ammonia to nitrite for energy acquisition in the presence of oxygen. Recent study has unraveled highly diverse sublineages within the previously defined AOA ecotypes (i.e., water column A (WCA) and water column B (WCB)), although the eco-physiology and environmental determinants of WCB subclades remain largely unclear. In this study, we examined the AOA communities along the water columns (40–3000 m depth) in the Costa Rica Dome (CRD) upwelling region in the eastern tropical North Pacific Ocean. Highly diverse AOA communities that were significantly different from those in oxygenated water layers were observed in the core layer of the oxygen minimum zone (OMZ), where the dissolved oxygen (DO) concentration was < 2μM. Moreover, a number of AOA phylotypes were found to be enriched in the OMZ core. Most of them were negatively correlated with DO and were also detected in other OMZs in the Arabian Sea and Gulf of California, which suggests low oxygen adaptation. This study provided the first insight into the differential niche partitioning and environmental determinants of various subclades within the ecotype WCB. Our results indicated that the ecotype WCB did indeed consist of various sublineages with different eco-physiologies, which should be further explored.

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Benthic phosphorus cycling in the Peruvian oxygen minimum zone

Biogeosciences ◽

10.5194/bg-13-1367-2016 ◽

2016 ◽

Vol 13 (5) ◽

pp. 1367-1386 ◽

Cited By ~ 12

Author(s):

Ulrike Lomnitz ◽

Stefan Sommer ◽

Andrew W. Dale ◽

Carolin R. Löscher ◽

Anna Noffke ◽

...

Keyword(s):

Water Column ◽

Surface Sediments ◽

Solid Phase ◽

Continental Margins ◽

Low Oxygen ◽

Anoxic Waters ◽

Oxygen Conditions ◽

Bottom Waters ◽

Minimum Zone ◽

Oxygen Minimum

Abstract. Oxygen minimum zones (OMZs) that impinge on continental margins favor the release of phosphorus (P) from the sediments to the water column, enhancing primary productivity and the maintenance or expansion of low-oxygen waters. A comprehensive field program in the Peruvian OMZ was undertaken to identify the sources of benthic P at six stations, including the analysis of particles from the water column, surface sediments, and pore fluids, as well as in situ benthic flux measurements. A major fraction of solid-phase P was bound as particulate inorganic P (PIP) both in the water column and in sediments. Sedimentary PIP increased with depth in the sediment at the expense of particulate organic P (POP). The ratio of particulate organic carbon (POC) to POP exceeded the Redfield ratio both in the water column (202 ± 29) and in surface sediments (303 ± 77). However, the POC to total particulate P (TPP = POP + PIP) ratio was close to Redfield in the water column (103 ± 9) and in sediment samples (102 ± 15). This suggests that the relative burial efficiencies of POC and TPP are similar under low-oxygen conditions and that the sediments underlying the anoxic waters on the Peru margin are not depleted in P compared to Redfield. Benthic fluxes of dissolved P were extremely high (up to 1.04 ± 0.31 mmol m−2 d−1), however, showing that a lack of oxygen promotes the intensified release of dissolved P from sediments, whilst preserving the POC / TPP burial ratio. Benthic dissolved P fluxes were always higher than the TPP rain rate to the seabed, which is proposed to be caused by transient P release by bacterial mats that had stored P during previous periods when bottom waters were less reducing. At one station located at the lower rim of the OMZ, dissolved P was taken up by the sediments, indicating ongoing phosphorite formation. This is further supported by decreasing porewater phosphate concentrations with sediment depth, whereas solid-phase P concentrations were comparatively high.

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Benthic phosphorus cycling in the Peruvian oxygen minimum zone

Biogeosciences Discussions ◽

10.5194/bgd-12-16755-2015 ◽

2015 ◽

Vol 12 (20) ◽

pp. 16755-16801 ◽

Cited By ~ 5

Author(s):

U. Lomnitz ◽

S. Sommer ◽

A. W. Dale ◽

C. R. Löscher ◽

A. Noffke ◽

...

Keyword(s):

Water Column ◽

Surface Sediments ◽

Solid Phase ◽

Continental Margins ◽

Low Oxygen ◽

Oxygen Minimum Zones ◽

Oxygen Conditions ◽

Bottom Waters ◽

Minimum Zone ◽

Oxygen Minimum

Abstract. Oxygen minimum zones (OMZs) that impinge on continental margins favor the release of phosphorus (P) from the sediments to the water column, enhancing primary productivity and the maintenance or expansion of low-oxygen waters. A comprehensive field program in the Peruvian OMZ was undertaken to identify the sources of benthic P, including the analysis of particles from the water column, surface sediments and pore fluids as well as in situ benthic flux measurements. A major fraction of solid phase P was bound as particulate inorganic P (PIP) both in the water column and in sediments. Sedimentary PIP increased with depth in the sediment at the expense of particulate organic P (POP). The ratio of particulate organic carbon (POC) to POP exceeded the Redfield Ratio both in the water column (202 ± 29) and in surface sediments (303 ± 77). However, the POC to total particulate P (TPP = POP + PIP) ratio was close to Redfield in the water column (103 ± 9) and in sediment samples (102 ± 15) taken from the core of the OMZ. This observation suggests that the burial efficiencies of POC and TPP are similar under the low oxygen conditions prevailing in the Peruvian OMZ. Benthic fluxes of dissolved P were extremely high (up to 1.04 ± 0.31 mmol m−2 d−1) and exceeded the fluxes resulting from the degradation of particulate organic matter raining to the seabed. Most of the excess P may have been released by bacterial mats that had stored P during previous periods when bottom waters were less reducing. At one station located at the lower rim of the OMZ, dissolved P was taken up by the sediments indicating recent phosphorite formation.

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Microbial communities and their biogeochemical role in the water column of the oxygen minimum zone in the eastern South Pacific

Gayana (Concepción) ◽

10.4067/s0717-65382006000300018 ◽

2006 ◽

Vol 70 ◽

Cited By ~ 2

Author(s):

Osvaldo Ulloa ◽

Lucy Belmar ◽

Laura Farías ◽

Maribel Castro-González ◽

Alexander Galán ◽

...

Keyword(s):

Microbial Communities ◽

Water Column ◽

South Pacific ◽

Oxygen Minimum Zone ◽

Minimum Zone ◽

Oxygen Minimum

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Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters

Applied and Environmental Microbiology ◽

10.1128/aem.03001-13 ◽

2013 ◽

Vol 80 (1) ◽

pp. 177-183 ◽

Cited By ~ 10

Author(s):

Lavane Kim ◽

Eulyn Pagaling ◽

Yi Y. Zuo ◽

Tao Yan

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Bacterial Species ◽

Community Analysis ◽

Microbial Community Analysis ◽

Rrna Gene ◽

Content Type ◽

Property Change ◽

And Control ◽

Start Ups

ABSTRACTThe impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected,BurkholderialesandRhodocyclalesof theBetaproteobacteriaclass were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes.

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Zooplankton fluctuations in Jurumirim Reservoir (São Paulo, Brazil): a three-year study

Brazilian Journal of Biology ◽

10.1590/s1519-69842009000100002 ◽

2009 ◽

Vol 69 (1) ◽

pp. 1-18 ◽

Cited By ~ 23

Author(s):

LP. Sartori ◽

MG. Nogueira ◽

R. Henry ◽

EM. Moretto

Keyword(s):

Water Column ◽

Oxygen Concentration ◽

Retention Time ◽

Sao Paulo ◽

Seasonal Effect ◽

São Paulo ◽

Low Oxygen ◽

High Concentration ◽

Heterogeneous Distribution ◽

Low Oxygen Concentration

During three consecutive years, monthly samples of zooplankton were taken in the lacustrine (dam) zone of Jurumirim (São Paulo, Brazil). The seasonal effect on basic limnological features (thermal regime, oxygen distribution, phytoplankton biomass, etc.) was also examined. The influence of the seasonality on the fluctuation of the zooplankton composition and abundance was not clearly detected (low degree of recurrent patterns). Rotifers (32 taxa) were the most abundant organisms during almost the entire study period with some seasonal alternations in the maximum abundance peaks of the main taxa (Conochilus unicornis, Keratella americana, K. cochlearis and Hexarthra spp.), except for Polyarthra (mainly P. vulgaris). Only occasionally copepods were numerically dominant. Higher copepod abundance was positively associated to periods of increase in the water retention time. Among the Copepoda (10 taxa) the calanoids (mainly Notodiaptomus iheringi) were more abundant, especially in warmer periods. Conversely, cyclopoids had higher abundance in autumn and winter. The species Thermocyclops minutus and T. decipiens co-occurred, but the first attained higher abundance. Some evidence of co-existence strategies between both species are considered. Cladocera (17 taxa) was never numerically dominant and the main taxa (Bosmina spp., Ceriodaphnia spp. and Diaphanosoma spp.) occurred almost the whole study period and did not present a seasonal pattern of fluctuation. Diaphanosoma (mainly D. birgei) attained the highest abundance among cladocerans. Most organisms were always found at the surface, but they also occupy the whole water column, even in periods of stratified conditions and low oxygen concentration in the bottom layers. Among the main zooplanktonic taxa, only Hexarthra avoids deep layers. An exceptionally high concentration of Copepoda nauplii on the surface was influenced by low transparency, high concentration of phytoplankton at this layer and low oxygen concentration at the bottom. In periods of higher retention timevariability there was a more heterogeneous distribution of the zooplankton in the water column. The increase in the retention time seems also to favor the copepod development. Finally, some inter-decade changes are considered on the basis of zooplankton assemblage structure observations.

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Modulation of the vertical particles transfer efficiency in the Oxygen Minimum Zone off Peru

10.5194/bg-2018-103 ◽

2018 ◽

Author(s):

Marine Bretagnon ◽

Aurélien Paulmier ◽

Véronique Garçon ◽

Boris Dewitte ◽

Sérena Illig ◽

...

Keyword(s):

Organic Matter ◽

Water Column ◽

Sediment Traps ◽

Biogeochemical Cycles ◽

High Temporal Resolution ◽

Oxygen Minimum Zones ◽

Marine Life ◽

Minimum Zone ◽

Earth’S System ◽

Oxygen Minimum

Abstract. The fate of the Organic Matter (OM) produced by marine life controls the major biogeochemical cycles of the Earth’s system. The OM produced through photosynthesis is either preserved, exported towards sediments or degraded through remineralisation in the water column. The productive Eastern Boundary Upwelling Systems (EBUSs) associated with Oxygen Minimum Zones (OMZs) should foster OM preservation due to low O2 conditions, but their intense and diverse microbial activity should enhance OM degradation. To investigate this contradiction, sediment traps were deployed near the oxycline and in the OMZ core on an instrumented moored line off Peru, providing high temporal resolution O2 series characterizing two seasonal steady states at the upper trap: suboxic ([O2]

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