Environmental microbiology

Removal of nutrients in denitrification system using coconut coir fibre for the biological treatment of aquaculture wastewater

by VR Manoj

Co-Authored by Prof.Namasivayam Vasudevan. Journal of Environmental Biology March 2012

Ideal bacterial support medium for fixed film denitrification processes/bioreactors must be inexpensive, durable and... more Ideal bacterial support medium for fixed film denitrification processes/bioreactors must be inexpensive, durable and possess large surface area with sufficient porosity. The present study has been focussed on removing nitrate nitrogen at two different nitrate nitrogen loading rates (60 (NLR I) and 120 (NLR II) mg l-1) from simulated aquaculture wastewater. Coconut coir fibre and a commercially available synthetic reticulated plastic media (Fujino Spirals) were used as packing medium in two independent upflow anaerobic packed bed column reactors. Removal of nitrate nitrogen was studied in correlation with other nutrients (COD, TKN, dissolved orthophosphate). Maximum removal of 97% at NLR-I and 99% at NLR – II of nitrate nitrogen was observed in with either media. Greater consistency in the case of COD removal of upto 81% was observed at NLR II where coconut coir was used as support medium compared to 72% COD removal by Fujino Spirals. The results observed indicate that the organic support medium is just as efficient in nitrate nitrogen removal as conventionally used synthetic support medium. The study is important as it specifically focuses on denitrification of aquaculture wastewater using cheaper organic support medium in anoxic bioreactors for the removal of nitrate nitrogen; which is seldom addressed as a significant problem.

Physical disturbance to ecological niches created by soil structure alters community composition of methanotrophs

by deepak kumaresan

ALIMENTOS EN EL CAMBIO CLIMATICO. Efectos en la Salud

by Ronnie Gavilan

In: Cambio Global España 2020/50. Cambio climático y salud. Centro Complutense de Estudios e Información Medioambiental. España

Pester_etal_2012_Frontiers

by Klaus-Holger Knorr

Freshwater wetlands are a major source of the greenhouse gas methane but at the same time can function as carbon sink.... more Freshwater wetlands are a major source of the greenhouse gas methane but at the same time can function as carbon sink. Their response to global warming and environmental pollution is one of the largest unknowns in the upcoming decades to centuries. In this review, we highlight the role of sulfate-reducing microorganisms (SRM) in the intertwined element cycles of wetlands. Although regarded primarily as methanogenic environments, biogeochemical studies have revealed a previously hidden sulfur cycle in wetlands that can sustain rapid renewal of the small standing pools of sulfate. Thus, dissimilatory sulfate reduction, which frequently occurs at rates comparable to marine surface sediments, can contribute up to 36–50% to anaerobic carbon mineralization in these ecosystems. Since sulfate reduction is thermodynamically favored relative to fermentative processes and methanogenesis, it effectively decreases gross methane production thereby mitigating the flux of methane to the atmosphere. However, very little is known about wetland SRM. Molecular analyses using dsrAB [encoding subunit A and B of the dissimilatory (bi)sulfite reductase] as marker genes demonstrated that members of novel phylogenetic lineages, which are unrelated to recognized SRM, dominate dsrAB richness and, if tested, are also abundant among the dsrAB-containing wetland microbiota. These discoveries point toward the existence of so far unknown SRM that are an important part of the autochthonous wetland microbiota. In addition to these numerically dominant microorganisms, a recent stable isotope probing study of SRM in a German peatland indicated that rare biosphere members might be highly active in situ and have a considerable stake in wetland sulfate reduction. The hidden sulfur cycle in wetlands and the fact that wetland SRM are not well represented by described SRM species explains their so far neglected role as important actors in carbon cycling and climate change.

Phylogenetic clustering increases with elevation for microbes

by jianjun wang

Jianjun Wang, Janne Soininen, Jizheng He, Ji Shen, Phylogenetic clustering increases with elevation in microbes, Environmental Microbiology Reports 4: 217-226.

Summary
Although phylogenetic approaches are useful for providing insights into the processes underlying... more Summary
Although phylogenetic approaches are useful for providing insights into the processes underlying biodiversity patterns, the studies of microbial phylogenetic relatedness are rare, especially for elevational gradients. Using high-throughput pyrosequencing, we examined the biodiversity patterns for biofilm bacterial communities that were scraped from stream stones along an elevational gradient from 1820 to 4050 m in China. The patterns of bacterial species richness and phylogenetic diversity were hollow towards higher elevations. The bacterial communities consisted of closer relatives than expected and displayed increasing terminal phylogenetic clustering towards mountain top. The increasing phylogenetic clustering with elevation contrasts reports for macroorganisms that revealed phylogenetic overdispersion at low or intermediate elevations. Because water temperature showed the strongest correlation with phylogenetic relatedness (r2 = 0.516), the elevational pattern in the bacterial phylogenetic structure indicated that environmental filtering possibly due to lower temperature or more frequent temperature fluctuations increased towards higher elevations. Evidence supporting the environmental filtering on bacteria was also reflected by the orderly succession in the relative abundance of different bacterial phyla along the elevational gradient and in the high evenness of bacterial taxa at higher elevations. Overall, our results indicated that ecological processes possibly related to temperature may play a dominant role in structuring bacterial biodiversity along the elevational gradient.

Keywords: Bacteria, Elevational gradient, Phylogenetic diversity, Phylogenetic relatedness, Species diversity pattern, Streams

mean nearest taxon distances: MNTD
mean nearest neighbor distance: MNND
standardized effect size of mean nearest taxon distances: ses.MNTD
nearest taxon index: NTI

Another new reference:
Stegen, J.C., Lin, X., Konopka, A.E., and Fredrickson, J.K. (2012) Stochastic and deterministic assembly processes in subsurface microbial communities. ISME J. In press.

Plant diversity improves protection against soil-borne pathogens by fostering antagonistic bacterial communities

by Alexandre Jousset

Co authored with Ellen Latz, Nico Eisenhauer, Stefan Scheu and Björn Rall

1. Rhizosphere bacteria antagonistic to fungal pathogens improve plant performance by prevent-
ing infection. In... more 1. Rhizosphere bacteria antagonistic to fungal pathogens improve plant performance by prevent-
ing infection. In temperate grasslands, primary productivity often increases with plant diversity,
and we hypothesized that this effect may in part rely on the interactions between plants and antago-
nistic bacteria.
2. We investigated the impact of plant diversity and functional group composition on soil bacteria
producing the antifungal compounds 2,4-diacetylphloroglucinol (DAPG) and pyrrolnitrin (PRN)
in a long-term grassland biodiversity experiment, as well as their impact on soil suppressiveness. Soil
suppressiveness was investigated in a model infection assay with Beta vulgaris and the pathogen
Rhizoctonia solani.
3. The abundance of DAPG and PRN producers increased with plant diversity and that of PRN
also increased in the presence of grasses. Moreover, legume species richness and coverage decreased
the abundance of DAPG and PRN producers, respectively, contrary to beneficial effects of legumes
on soil microorganisms reported previously. In turn, soil suppressiveness was at maximum when
DAPG and PRN producer abundance was high.
4. Synthesis. Our results suggest that plant diversity contributes to plant community resistance
against pathogens by fostering beneficial bacterial communities. This indirect soil feedback mecha-
nism may contribute to the positive relationship between plant diversity and productivity and could
also help the development of more sustainable and environmentally friendly agricultural manage-
ment strategies.

Application of the denaturing gradient gel electrophoresis (DGGE) technique as an efficient diagnostic tool for ciliate communities in soil

by Alexandre Jousset

Ecological and evolutive implications of bacterial defences against predators

by Alexandre Jousset

The Impact of Land-Use Practices on Soil Microbes

by Tom Sizmur

Viral communities associated with healthy and bleaching corals

by Kristen Marhaver

Microbial to reef scale interactions between the reef-building coral Montastraea annularis and benthic algae

by Kristen Marhaver

Metabolic strategies deployed by Pseudomonas fluorescens to combat metal pollutants: Biotechnological prospects

by Joe Lemire

Persistence of a biocontrol Pseudomonas inoculant as high populations of culturable and non-culturable cells in 200-cm-deep soil profiles

by Miro Svercel

doi:10.1016/j.soilbio.2011.09.020

Little is known about the ecology of soil inoculants used for pathogen biocontrol, biofertilization and bioremediation... more Little is known about the ecology of soil inoculants used for pathogen biocontrol, biofertilization and bioremediation under field conditions. We investigated the persistence and the physiological states of soil-inoculated Pseudomonas protegens (previously Pseudomonas fluorescens) CHA0 (108 CFU g−1 surface soil) in different soil microbial habitats in a planted ley (Medicago sativa L.) and an uncovered field plot. At 72 days, colony counts of the inoculant were low in surface soil (uncovered plot) and earthworm guts (ley plot), whereas soil above the plow pan (uncovered plot), and the rhizosphere and worm burrows present until 1.2 m depth (ley plot) were survival hot spots (105–106 CFU g−1 soil). Interestingly, strain CHA0 was also detected in the subsoil of both plots, at 102–105 CFU g−1 soil between 1.8 and 2 m depth. However, non-cultured CHA0 cells were also evidenced based on immunofluorescence microscopy. Kogure's direct viable counts of nutrient-responsive cells showed that many more CHA0 cells were in a viable but non-culturable (VBNC) or a non-responsive (dormant) state than in a culturable state, and the proportion of cells in those non-cultured states depended on soil microbial habitat. At the most, cells in a VBNC state amounted to 34% (above the plow pan) and those in a dormant state to 89% (in bulk soil between 0.6 and 2 m) of all CHA0 cells. The results indicate that field-released Pseudomonas inoculants may persist at high cell numbers, even in deeper soil layers, and display a combination of different physiological states whose prevalence fluctuates according to soil microbial habitats.

Pseudomonas syringae pv. syringae B728a hydrolyses indole‐3‐acetonitrile to the plant hormone indole‐3‐acetic acid

by Arantza Rico

Erwinia amylovora strains from outbreaks of fire blight in Spain: phenotypic characteristics

by Arantza Rico

Closely related protist strains have different grazing impacts on natural bacterial communities

by Edvard Glücksman

Environ Microbiol. 2010 Dec;12(12):3105-13

Glücksman E, Bell T, Griffiths RI, Bass D.

Department... more Environ Microbiol. 2010 Dec;12(12):3105-13

Glücksman E, Bell T, Griffiths RI, Bass D.

Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.

Abstract
Summary Heterotrophic protists are abundant in most environments and exert a strong top-down control on bacterial communities. However, little is known about how selective most protists are with respect to their bacterial prey. We conducted feeding trials using cercomonad and glissomonad Cercozoa by assaying them on a standardized, diverse bacterial community washed from beech leaf litter. For each of the nine protist strains assayed here, we measured several phenotypic traits (cell volume, speed, plasticity and protist cell density) that we anticipated would be important for their feeding ecology. We also estimated the genetic relatedness of the strains based on the 18S rRNA gene. We found that the nine protist strains had significantly different impacts on both the abundance and the composition of the bacterial communities. Both the phylogenetic distance between protist strains and differences in protist strain traits were important in explaining variation in the bacterial communities. Of the morphological traits that we investigated, protist cell volume and morphological plasticity (the extent to which cells showed amoeboid cell shape flexibility) were most important in determining bacterial community composition. The results demonstrate that closely related and morphologically similar protist species can have different impacts on their prey base.

El impacto de los pozos sépticos en la calidad de agua y los arrecifes de coral en la Reserva Marina de Tres Palmas (Rincón-Puerto Rico)

by Edwin A. Hernández-Delgado

Norat Ramírez, J., P. Méndez Lázaro, E.A. Hernández Delgado, & L. Cordero Rivera. El impacto de los pozos sépticos en la calidad de agua y los arrecifes de coral en la Reserva Marina de Tres Palmas (Rincón-Puerto Rico). IX Congreso Regional para Norteamérica y el Caribe sobre Ingeniería Sanitaria y Ambiental – Región I de AIDIS (in press)

Sewage impacts in coral reef ecosystems are a major concern. Previous study showed evidence that coral reefs along a... more Sewage impacts in coral reef ecosystems are a major concern. Previous study showed evidence that coral reefs along a significant portion of the southwestern Puerto Rico shelf are being severely impacted by nonpoint source sewage pollution, mostly from inadequate septic tanks. In this project we analyzed the impact of nonpoint source water pollution on water quality and coral reefs in coastal waters of the Tres Palmas Marine Reserve in Rincón. Both inorganic and microbiological marine water quality indicators were used as impact parameters. The analysis of nonpoint pollution sources was carried out through the use of Remote Sensing and Geographic Information Systems techniques and land based water sampling. For coral reef evaluation, we randomly selected 54 sampling stations at each survey area within and outside the Tres Palmas Marine Reserve subdivided on 9 replicate stations per site. The presence of threatened Elkhorn coral, Acropora palmata and dead standing skeletons within each 100 m2 plot was noted.  Average densities detected in coastal water stations within or near the Tres Palmas Reserve ranged from 0.1 to 15.3 CFU/100 mL of Faecal coliforms and 5 to 27 CFU/100 mL of Enterococci, but occasional pulses exceeded legal standards. This confirms the presence of microbiological contamination by rainfall runoff and possible overflows of septic tanks located close to the coast. Most residences along the Tres Palmas Marine Reserve coastal watersheds use septic tanks. Intermittent creeks serve as conduits of septic tank overflows or bypass discharges from several "barriadas" within the selected sub-watersheds. The analysis of 223 colonies of A. palmata suggests that corals are showing unmistakable historical signs of partial mortality of colonies associated with recurrent rainfall runoff.

Practical approaches to sterility testing

by Tim Sandle

In Search of an Uncultured Human-Associated TM7 Bacterium in the Environment

by Hazel Ozuna

We have identified an environmental bacterium in the Candidate Division TM7 with $98.5% 16S rDNA gene homology to amore We have identified an environmental bacterium in the Candidate Division TM7 with $98.5% 16S rDNA gene homology to a
group of TM7 bacteria associated with the human oral cavity and skin. The environmental TM7 bacterium (referred to as
TM7a-like) was readily detectable in wastewater with molecular techniques over two years of sampling. We present the first
images of TM7a-like cells through FISH technique and the first images of any TM7 as viable cells through the STARFISH
technique. In situ quantification showed TM7 concentration in wastewater up to five times greater than in human oral sites.
We speculate that upon further characterization of the physiology and genetics of the TM7a-like bacterium from
environmental sources and confirmation of its genomic identity to human-associated counterparts it will serve as model
organisms to better understand its role in human health. The approach proposed circumvents difficulties imposed by
sampling humans, provides an alternative strategy to characterizing some diseases of unknown etiology, and renders a much needed understanding of the ecophysiological role hundreds of unique Bacteria and Archaea strains play in mixed
microbial communities.

Gain and loss of phototrophic genes revealed by comparison of two Citromicrobium bacterial genomes

by Paul Fogg

Submitted