Extraction of Total DNA and RNA from Marine Filter Samples and Generation of a Universal cDNA as Universal Template for Marker Gene Studies.

Microbial communities play an important role in marine ecosystem processes. Although the number of studies targeting marker genes such as the 16S rRNA gene has increased during the last years, the vast majority of marine diversity are rather unexplored. Moreover, most studies focused on the entire microbial community and thus do not assess the active fraction of the microbial community. Here, we describe a detailed protocol for the simultaneous extraction of DNA and RNA from marine water samples and the generation of cDNA from the isolated RNA that can be used as a universal template in various marker gene studies.

Complete Genome Sequence of Alkalihalobacillus sp. Strain LMS39, a Haloalkaliphilic Bacterium Isolated from a Hypersaline Lake.

Here, we report the complete genome sequence of a haloalkaliphilic bacterium (Alkalihalobacillus sp. strain LMS39) isolated from Lake Magadi, a hypersaline lake in Kenya. The genome comprised 4,850,562 bp with a GC content of 37%.

Significance of gene variants for the functional biogeography of the near-surface Atlantic Ocean microbiome.

Microbial communities are major drivers of global elemental cycles in the oceans due to their high abundance and enormous taxonomic and functional diversity. Recent studies assessed microbial taxonomic and functional biogeography in global oceans but microbial functional biogeography remains poorly studied. Here we show that in the near-surface Atlantic and Southern Ocean between 62°S and 47°N microbial communities exhibit distinct taxonomic and functional adaptations to regional environmental conditions. Richness and diversity showed maxima around 40° latitude and intermediate temperatures, especially in functional genes (KEGG-orthologues, KOs) and gene profiles. A cluster analysis yielded three clusters of KOs but five clusters of genes differing in the abundance of genes involved in nutrient and energy acquisition. Gene profiles showed much higher distance-decay rates than KO and taxonomic profiles. Biotic factors were identified as highly influential in explaining the observed patterns in the functional profiles, whereas temperature and biogeographic province mainly explained the observed taxonomic patterns. Our results thus indicate fine-tuned genetic adaptions of microbial communities to regional biotic and environmental conditions in the Atlantic and Southern Ocean.

The cropping system matters - Contrasting responses of winter faba bean (Vicia faba L.) genotypes to drought stress.

Intercropping of legumes and cereals provides many ecological advantages and contributes to a sustainable agriculture. These agricultural systems face ongoing shifts in precipitation patterns and seasonal drought. Although the effect of drought stress on legumes has been frequently studied, knowledge about water deficits influencing legumes under different cropping systems is still limited. Therefore, we investigated the impact of water deficit and re-irrigation on two winter faba bean genotypes (S_004 and S_062) and winter wheat (var. Genius) in pure and intercropped stands under greenhouse conditions. Various physiological and biochemical parameters, such as canopy surface temperature, leaf relative water content and proline content, were collected at three time points (beginning of water deficit, end of water deficit, after re-irrigation). In addition, water use efficiency (WUE) was analyzed at the end of the experiment. The overall drought stress tolerance was determined as conceptual analysis of all measured parameters. Water deficit significantly affected WUE, surface temperature and proline content of both winter faba bean genotypes. Interestingly, intercropping with wheat resulted in an overall high drought tolerance of genotype S_004, while genotype S_062 had a high drought tolerance in pure stands. Under water deficit, pure stands of S_062 substantially increased WUE by 30.5%. Intercropping of genotype S_004 increased the dry matter per plant by 31.7% compared to pure stands under water deficit. Contrary, intercropping of genotype S_062 did not improve the dry matter production. Our findings indicate that genotype S_004 benefits from resource complementarity in intercropping systems with wheat, whereas S_062 is better suitable for pure stands due to competitive effects. Thus, our study highlights that the drought tolerance of winter faba bean genotypes depends on the cropping system, leading to a demand for drought-adapted cultivars specifically selected for intercropping.

Morphological and Metabolite Responses of Potatoes under Various Phosphorus Levels and Their Amelioration by Plant Growth-Promoting Rhizobacteria.

Low phosphorus (P) availability is a major limiting factor for potatoes. P fertilizer is applied to enhance P availability; however, it may become toxic when plants accumulate at high concentrations. Therefore, it is necessary to gain more knowledge of the morphological and biochemical processes associated with P deficiency and toxicity for potatoes, as well as to explore an alternative approach to ameliorate the P deficiency condition. A comprehensive study was conducted (I) to assess plant morphology, mineral allocation, and metabolites of potatoes in response to P deficiency and toxicity; and (II) to evaluate the potency of plant growth-promoting rhizobacteria (PGPR) in improving plant biomass, P uptake, and metabolites at low P levels. The results revealed a reduction in plant height and biomass by 60-80% under P deficiency compared to P optimum. P deficiency and toxicity conditions also altered the mineral concentration and allocation in plants due to nutrient imbalance. The stress induced by both P deficiency and toxicity was evident from an accumulation of proline and total free amino acids in young leaves and roots. Furthermore, root metabolite profiling revealed that P deficiency reduced sugars by 50-80% and organic acids by 20-90%, but increased amino acids by 1.5-14.8 times. However, the effect of P toxicity on metabolic changes in roots was less pronounced. Under P deficiency, PGPR significantly improved the root and shoot biomass, total root length, and root surface area by 32-45%. This finding suggests the potency of PGPR inoculation to increase potato plant tolerance under P deficiency.

The Effects of Cropping Regimes on Fungal and Bacterial Communities of Wheat and Faba Bean in a Greenhouse Pot Experiment Differ between Plant Species and Compartment.

Many bacteria and fungi in the plant rhizosphere and endosphere are beneficial to plant nutrient acquisition, health, and growth. Although playing essential roles in ecosystem functioning, our knowledge about the effects of multiple cropping regimes on the plant microbiome and their interactions is still limited. Here, we designed a pot experiment simulating different cropping regimes. For this purpose, wheat and faba bean plants were grown under controlled greenhouse conditions in monocultures and in two intercropping regimes: row and mixed intercropping. Bacterial and fungal communities in bulk and rhizosphere soils as well as in the roots and aerial plant parts were analyzed using large-scale metabarcoding. We detected differences in microbial richness and diversity between the cropping regimes. Generally, observed effects were attributed to differences between mixed and row intercropping or mixed intercropping and monoculture. Bacterial and fungal diversity were significantly higher in bulk soil samples of wheat and faba bean grown in mixed compared to row intercropping. Moreover, microbial communities varied between crop species and plant compartments resulting in different responses of these communities toward cropping regimes. Leaf endophytes were not affected by cropping regime but bacterial and fungal community structures in bulk and rhizosphere soil as well as fungal community structures in roots. We further recorded highly complex changes in microbial interactions. The number of negative inter-domain correlations between fungi and bacteria decreased in bulk and rhizosphere soil in intercropping regimes compared to monocultures due to beneficial effects. In addition, we observed plant species-dependent differences indicating that intra- and interspecific competition between plants had different effects on the plant species and thus on their associated microbial communities. To our knowledge, this is the first study investigating microbial communities in different plant compartments with respect to multiple cropping regimes using large-scale metabarcoding. Although a simple design simulating different cropping regimes was used, obtained results contribute to the understanding how cropping regimes affect bacterial and fungal communities and their interactions in different plant compartments. Nonetheless, we need field experiments to properly quantify observed effects in natural ecosystems.

Extraction of Total DNA and RNA from Marine Filter Samples and Generation of a cDNA as Universal Template for Marker Gene Studies.

Microbial communities play an important role in marine ecosystem processes. Although the number of studies targeting marker genes such as the 16S rRNA gene has been increased in the last few years, the vast majority of marine diversity is rather unexplored. Moreover, most studies focused on the entire bacterial community and thus disregarded active microbial community players. Here, we describe a detailed protocol for the simultaneous extraction of DNA and RNA from marine water samples and for the generation of cDNA from the isolated RNA which can be used as a universal template in various marker gene studies.

Fine Spatial Scale Variation of Soil Microbial Communities under European Beech and Norway Spruce.

The complex interactions between trees and soil microbes in forests as well as their inherent seasonal and spatial variations are poorly understood. In this study, we analyzed the effects of major European tree species (Fagus sylvatica L. and Picea abies (L.) Karst) on soil bacterial and fungal communities. Mineral soil samples were collected from different depths (0-10, 10-20 cm) and at different horizontal distances from beech or spruce trunks (0.5, 1.5, 2.5, 3.5 m) in early summer and autumn. We assessed the composition of soil bacterial and fungal communities based on 16S rRNA gene and ITS DNA sequences. Community composition of bacteria and fungi was most strongly affected by soil pH and tree species. Different ectomycorrhizal fungi (e.g., Tylospora) known to establish mutualistic associations with plant roots showed a tree species preference. Moreover, bacterial and fungal community composition showed spatial and seasonal shifts in soil surrounding beech and spruce. The relative abundance of saprotrophic fungi was higher at a depth of 0-10 vs. 10-20 cm depth. This was presumably a result of changes in nutrient availability, as litter input and organic carbon content decreased with soil depth. Overall bacterial community composition showed strong variations under spruce with increasing distance from the tree trunks, which might be attributed in part to higher fine root biomass near spruce trunks. Furthermore, overall bacterial community composition was strongly affected by season under deciduous trees.

Spatial and temporal heterogeneity of ventilator-associated lung injury after surfactant depletion.

Volutrauma and atelectrauma have been proposed as mechanisms of ventilator-associated lung injury, but few studies have compared their relative importance in mediating lung injury. The objective of our study was to compare the injury produced by stretch (volutrauma) vs. cyclical recruitment (atelectrauma) after surfactant depletion. In saline-lavaged rabbits, we used high tidal volume, low respiratory rate, and low positive end-expiratory pressure to produce stretch injury in nondependent lung regions and cyclical recruitment in dependent lung regions. Tidal changes in shunt fraction were assessed by measuring arterial Po(2) oscillations. After ventilating for times ranging from 0 to 6 h, lungs were excised, sectioned gravitationally, and assessed for regional injury by evaluation of edema formation, chemokine expression, upregulation of inflammatory enzyme activity, and alveolar neutrophil accumulation. Edema formation, lung tissue interleukin-8 expression, and alveolar neutrophil accumulation progressed more rapidly in dependent lung regions, whereas macrophage chemotactic protein-1 expression progressed more rapidly in nondependent lung regions. Temporal and regional heterogeneity of lung injury were substantial. In this surfactant depletion model of acute lung injury, cyclical recruitment produced more injury than stretch.

Quantitative distributions of Epsilonproteobacteria and a Sulfurimonas subgroup in pelagic redoxclines of the central Baltic Sea.

Members of the class Epsilonproteobacteria are known to be of major importance in biogeochemical processes at oxic-anoxic interfaces. In pelagic redoxclines of the central Baltic Sea, an uncultured epsilonproteobacterium related to Sulfurimonas denitrificans was proposed to play a key role in chemolithotrophic denitrification (I. Brettar, M. Labrenz, S. Flavier, J. Bötel, H. Kuosa, R. Christen, and M. G. Höfle, Appl. Environ. Microbiol. 72:1364-1372, 2006). In order to determine the abundance, activity, and vertical distribution of this bacterium in high-resolution profiles, 16S rRNA cloning and catalyzed reporter deposition and fluorescence in situ hybridization (CARD-FISH) and quantitative PCR measurements were carried out. The results showed that 21% of the derived clone sequences, which in the present study were grouped together under the name GD17, had >99% similarity to the uncultured epsilonproteobacterium. A specific gene probe against GD17 (S-*-Sul-0090-a-A-18) was developed and used for enumeration by CARD-FISH. In different pelagic redoxclines sampled during August 2003, May 2005, and February 2006, GD17 cells were always detected from the lower oxic area to the sulfidic area. Maximal abundance was detected around the chemocline, where sulfide and nitrate concentrations were close to the detection limit. The highest GD17 numbers (2 x 10(5) cells ml(-1)), representing up to 15% of the total bacteria, were comparable to those reported for Epsilonproteobacteria in pelagic redoxclines of the Black Sea and the Cariaco Trench (X. Lin, S. G. Wakeham, I. F. Putnam, Y. M. Astor, M. I. Scranton, A. Y. Chistoserdov, and G. T. Taylor, Appl. Environ. Microbiol. 72:2679-2690, 2006). However, in the Baltic Sea redoxclines, Epsilonproteobacteria consisted nearly entirely of cells belonging to the distinct GD17 group. This suggested that GD17 was the best-adapted epsilonproteobacterium within this ecological niche.

The implications of arterial Po2 oscillations for conventional arterial blood gas analysis.

In a surfactant-depletion model of lung injury, tidal recruitment of atelectasis and changes in shunt fraction lead to large Pao2 oscillations. We investigated the effect of these oscillations on conventional arterial blood gas (ABG) results using different sampling techniques in ventilated rabbits. In each rabbit, 5 different ventilator settings were studied, 2 before saline lavage injury and 3 after lavage injury. Ventilator settings were altered according to 5 different goals for the amplitude and mean value of brachiocephalic Pao2 oscillations, as guided by a fast responding intraarterial probe. ABG collection was timed to obtain the sample at the peak or trough of the Pao2 oscillations, or over several respiratory cycles. Before lung injury, oscillations were small and sample timing did not influence Pao2. After saline lavage, when Po2 fluctuations measured by the indwelling arterial Po2 probe confirmed tidal recruitment, Pao2 by ABG was significantly higher at peak (295 +/- 130 mm Hg) compared with trough (74 +/- 15 mm Hg) or mean (125 +/- 75 mm Hg). In early, mild lung injury after saline lavage, Pao2 can vary markedly during the respiratory cycle. When atelectasis is recruited with each breath, interpretation of changes in shunt fraction, based on conventional ABG analysis, should account for potentially large respiratory variations in arterial Po2.

Effects of respiratory rate, plateau pressure, and positive end-expiratory pressure on PaO2 oscillations after saline lavage.

One of the proposed mechanisms of ventilator-associated lung injury is cyclic recruitment of atelectasis. Collapse of dependent lung regions with every breath should lead to large oscillations in PaO2 as shunt varies throughout the respiratory cycle. We placed a fluorescence-quenching PO2 probe in the brachiocephalic artery of six anesthetized rabbits after saline lavage. Using pressure-controlled ventilation with oxygen, ventilator settings were varied in random order over three levels of positive end-expiratory pressure (PEEP), respiratory rate (RR), and plateau pressure minus PEEP (Delta). Dependence of the amplitude of PaO2 oscillations on PEEP, RR, and Delta was modeled by multiple linear regression. Before lavage, arterial PO2 oscillations varied from 3 to 22 mm Hg. After lavage, arterial PO2 oscillations varied from 5 to 439 mm Hg. Response surfaces showed markedly nonlinear dependence of amplitude on PEEP, RR, and Delta. The large PaO2 oscillations observed provide evidence for cyclic recruitment in this model of lung injury. The important effect of RR on the magnitude of PaO2 oscillations suggests that the static behavior of atelectasis cannot be accurately extrapolated to predict dynamic behavior at realistic breathing frequencies.

Mechanical ventilation with permissive hypercapnia increases intrapulmonary shunt in septic and nonseptic patients with acute respiratory distress syndrome.

OBJECTIVE: To compare the effects of conventional mechanical ventilation with low-volume, pressure-limited ventilation (LVPLV) and permissive hypercapnia on ventilation-perfusion (V/Q) distributions in patients with acute respiratory distress syndrome. We hypothesized that the advantageous cardiopulmonary effects of LVPLV would be greater in patients with sepsis than in those without sepsis. PATIENTS AND INTERVENTIONS: Twenty-two patients with acute respiratory distress syndrome were studied (group 1: 12 patients with hyperdynamic sepsis; group 2: 10 nonseptic patients). Intrapulmonary shunt (Qsp/Qt) (percentage of cardiac output), perfusion of "low" V/Q areas (percentage of cardiac output), ventilation of "high" V/Q areas (percentage of total ventilation [VE]), and deadspace ventilation (percentage of VE) were calculated from the retention/excretion data of six inert gases. Data were obtained during conventional mechanical ventilation and during LVPLV. MEASUREMENTS AND MAIN RESULTS: In group 1, LVPLV increased PaCO(0)rom 38 +/- 6 torr (5.1 +/- 0.8 kPa) to 61 +/- 12 torr (8.1 +/- 1.6 kPa). Qsp/Qt increased from 28 +/- 16% to 36 +/- 17%, whereas Pao2 (84 +/- 15 torr [11.1 +/- 2.0 kPa] vs. 86 +/- 21 torr [11.5 +/- 2.8 kPa]) and Qt (10.6 +/- 2.3 vs. 11.5 +/- 2.5 L x -1) remained unchanged and PVO(2) (40 +/- 4 [5.3 +/- 0.5 kPa] vs. 49 +/- 6 torr [6.5 +/- 0.3]) increased. In group 2, LVPLV increased PaCO(2) from 38 +/- 6 torr (5.1 +/- 0.8 kPa) to 63 +/- 11 torr (8.4 +/- 1.5 kPa). For Qsp/Qt (24 +/- 9% to 34 +/- 16%), the increase was not significant, whereas Qt (7.4 +/- 1.8 vs. 10.2 +/- 2.2 L x -1), PVO(2)(38 +/- 4 torr [5.1 +/- 0.5 kPa] vs. 50 +/- 6 mm Hg [6.7 +/- 0.8 kPa]), and PaO(2) (89 +/- 16 torr [11.9 +/- 2.1 kPa] vs. 98 +/- 19 torr [13.1 +/- 2.5 kPa]) increased. In both groups, the scatter of perfusion distribution (log SDQ) was greater than expected for normal subjects but was not different between the groups or altered by the treatments. CONCLUSIONS: In patients with acute respiratory distress syndrome, LVPLV with permissive hypercapnia, tended to increase Qsp/Qt, without a concomitant decrease of PaO(2). This occurs because, although atelectasis and increased shunt result from the low ventilatory volume, the effects on PaO(2) are offset by increased PVO(2) resulting from the hypercapnic stimulation of cardiac output. This result was independent of the presence or absence of sepsis.