Salinity-independent dissipation of antibiotics from flooded tropical soil: a microcosm study

River deltas are frequently facing salinity intrusion, thus challenging agricultural production in these areas. One adaption strategy to increasing salinity is shrimp production, which however, heavily relies on antibiotic usage. This study was performed to evaluate the effect of increasing salinity on the dissipation rates of antibiotics in tropical flooded soil systems. For this purpose, paddy top soil from a coastal Vietnamese delta was spiked with selected frequently used antibiotics (sulfadiazine, sulfamethazine, sulfamethoxazole, trimethoprim) and incubated with flood water of different salt concentrations (0, 10, 20 g L−1). Antibiotic concentrations were monitored in water and soil phases over a period of 112 days using liquid chromatography and tandem mass spectrometry. We found that sulfamethazine was the most persistent antibiotic in the flooded soil system (DT50 = 77 days), followed by sulfadiazine (DT50 = 53 days), trimethoprim (DT50 = 3 days) and sulfamethoxazole (DT50 = 1 days). With the exception of sulfamethoxazole, the apparent distribution coefficient increased significantly (p < 0.05) for all antibiotics in course of the incubation, which indicates an accumulation of antibiotics in soil. On a whole system basis, including soil and water into the assessment, there was no overall salinity effect on the dissipation rates of antibiotics, suggesting that common e-fate models remain valid under varying salinity

Arad'ın resimleri

Taha Toros Arşivi, Dosya No: 43-Agop AradUnutma İstanbul projesi İstanbul Kalkınma Ajansı'nın 2016 yılı "Yenilikçi ve Yaratıcı İstanbul Mali Destek Programı" kapsamında desteklenmiştir. Proje No: TR10/16/YNY/010

Draft Genome Sequences of Two Gammaproteobacterial Methanotrophs Isolated from Rice Ecosystems

The genomes of the aerobic methanotrophs “Methyloterricola oryzae” strain 73aT and Methylomagnum ishizawai strain 175 were sequenced. Both strains were isolated from rice plants. Methyloterricola oryzae strain 73aT represents the first isolate of rice paddy cluster I, and strain 175 is the second representative of the recently described genus Methylomagnum

Microbial Response to Experimentally Controlled Redox Transitions at the Sediment Water Interface.

The sediment-water interface of freshwater lakes is characterized by sharp chemical gradients, shaped by the interplay between physical, chemical and microbial processes. As dissolved oxygen is depleted in the uppermost sediment, the availability of alternative electron acceptors, e.g. nitrate and sulfate, becomes the limiting factor. We performed a time series experiment in a mesocosm to simulate the transition from aerobic to anaerobic conditions at the sediment-water interface. Our goal was to identify changes in the microbial activity due to redox transitions induced by successive depletion of available electron acceptors. Monitoring critical hydrochemical parameters in the overlying water in conjunction with a new sampling strategy for sediment bacteria enabled us to correlate redox changes in the water to shifts in the active microbial community and the expression of functional genes representing specific redox-dependent microbial processes. Our results show that during several transitions from oxic-heterotrophic condition to sulfate-reducing condition, nitrate-availability and the on-set of sulfate reduction strongly affected the corresponding functional gene expression. There was evidence of anaerobic methane oxidation with NOx. DGGE analysis revealed redox-related changes in microbial activity and expression of functional genes involved in sulfate and nitrite reduction, whereas methanogenesis and methanotrophy showed only minor changes during redox transitions. The combination of high-frequency chemical measurements and molecular methods provide new insights into the temporal dynamics of the interplay between microbial activity and specific redox transitions at the sediment-water interface

Evidence for signatures of ancient microbial life in paleosols

Loess-paleosol sequences are terrestrial archives of past climate change. They may host traces of ancient microbial life, but little information is available on the recovery of microbial biomarkers from such deposits. We hypothesized that microbial communities in soil horizons up to an age of 127 kyr carry information related to past environments. We extracted DNA from a loess-paleosol sequence near Toshan, Northern Iran, with 26 m thick deposits showing different degrees of soil development, performed quantitative PCR and 16S rRNA gene amplicon sequencing. Periods of soil formation archived within the loess sediment led to higher diversity and bacterial abundance in the paleosol horizons. Community composition fluctuated over the loess-paleosol sequence and was mainly correlated with age and depth, (ADONIS R-2 < 0.14, P <= 0.002), while responses to paleosol soil traits were weaker. Phyla like Bacteriodetes, Proteobacteria or Acidobacteria were more prevalent in paleosol horizons characterized by intense soil formation, while weakly developed paleosols or loess horizons hosted a higher percentage and diversity of Actinobacteria. Taken together, our findings indicate that the microbial community in loess-paleosol sequences carries signatures of earlier environmental conditions that are preserved until today

Paradox reconsidered: Methane oversaturation in well-oxygenated lake waters

The widely reported paradox of methane oversaturation in oxygenated water challenges the prevailing paradigm that microbial methanogenesis only occurs under anoxic conditions. Using a combination of field sampling, incubation experiments, and modeling, we show that the recurring mid-water methane peak in Lake Stechlin, northeast Germany, was not dependent on methane input from the littoral zone or bottom sediment or on the presence of known micro-anoxic zones. The methane peak repeatedly overlapped with oxygen oversaturation in the seasonal thermocline. Incubation experiments and isotope analysis indicated active methane production, which was likely linked to photosynthesis and/or nitrogen fixation within the oxygenated water, whereas lessening of methane oxidation by light allowed accumulation of methane in the oxygen-rich upper layer. Estimated methane efflux from the surface water was up to 5 mmol m−2 d−1. Mid-water methane oversaturation was also observed in nine other lakes that collectively showed a strongly negative gradient of methane concentration within 0–20% dissolved oxygen (DO) in the bottom water, and a positive gradient within ≥ 20% DO in the upper water column. Further investigation into the responsible organisms and biochemical pathways will help improve our understanding of the global methane cycle

Data_Sheet_1_Crop Rotation and Straw Application Impact Microbial Communities in Italian and Philippine Soils and the Rhizosphere of Zea mays.pdf

<p>Rice is one of the most important nourishments and its cultivation binds large agricultural areas in the world. Its cultivation leads to huge water consumption and high methane emissions. To diminish these problems, crop rotation between paddy rice and maize is introduced in Asia, but can lead to losses of carbon and water by the formation of desiccation cracks. To counteract these problems rice straw can be applied. We analyzed soil microbial responses to different crop rotation systems [rice–rice (RR), maize–maize (MM), maize–rice (MR)] and to rice straw application in the soil and rhizosphere of maize. Zea mays was grown in microcosms using soils from different field locations, each including different crop rotation regimes. The bacterial and fungal community composition was analyzed by 16S rRNA gene and ITS based amplicon sequencing in the bulk soil and rhizosphere. The microbiota was clearly different in soils from the different field locations (analysis of similarity, ANOSIM: R = 0.516 for the bacterial community; R = 0.817 for the fungal community). Within the field locations, crop rotation contributed differently to the variation in microbial community composition. Strong differences were observed in communities inhabiting soils under monosuccession (RR vs. MM) (ANOSIM: R = 0.923 for the bacterial and R = 0.714 for the fungal community), while the communities in soils undergoing MR crop rotation were more similar to those of the corresponding RR soils (ANOSIM: R = 0.111–0.175). The observed differences could be explained by altered oxygen availabilities in RR and MR soils, resulting in an enrichment of anaerobic bacteria in the soils, and the presence of the different crops, leading to the enrichment of host-plant specific microbial communities. The responses of the microbial communities to the application of rice straw in the microcosms were rather weak compared to the other factors. The taxa responding in bulk soil and rhizosphere were mostly distinct. In conclusion, this study revealed that the different agricultural management practices affect microbial community composition to different extent, not only in the bulk soil but also in the rhizosphere, and that the microbial responses in bulk soil and rhizosphere are distinct.</p

NMDS plot (stress 0.13) of 16S rRNA bacterial DGGE banding patterns.

<p>Arrows indicate the direction triggered by methane and nitrate as the strongest analyzed environmental factors. Ellipses indicate a confidence interval of 95% and ANOSIM analysis was significant (p = 0.001, r = 0.558). Colors indicate the six transitions phases (TP): red = TP 1 (Transition from oxygen to nitrate as electron acceptor), green = TP 2 (Short oxic pulse), yellow = TP 3 (nitrate depletion and sulfide development), light blue = TP 4 (Nitrate additions under sulfidic condition), dark blue = sulfidic phase, purple = oxic phase.</p