Changes in bacterial community composition and dynamics and viral mortality rates associated with enhanced flagellate grazing in a mesoeutrophic reservoir

Bacterioplankton from a meso-eutrophic dam reservoir was size fractionated to reduce (80% of the total bacteria by the end of the experiment. Once again, BCC changed strongly and a significant fraction of the large filaments was detected using a FISH probe targeted to members of the Flectobacillus lineage. Shifts of BCC were also reflected in DGGE patterns and in the increases in the relative importance of both beta proteobacteria and members of the Cytophaga-Flavobacterium cluster, which consistently formed different parts of the bacterial flocs. Viral concentrations and frequencies of infected cells were highly significantly correlated with grazing rates, suggesting that protistan grazing may stimulate viral activity

The Passive Yet Successful Way of Planktonic Life: Genomic and Experimental Analysis of the Ecology of a Free-Living Polynucleobacter Population

Background: The bacterial taxon Polynucleobacter necessarius subspecies asymbioticus represents a group of planktonic freshwater bacteria with cosmopolitan and ubiquitous distribution in standing freshwater habitats. These bacteria comprise,1 % to 70 % (on average about 20%) of total bacterioplankton cells in various freshwater habitats. The ubiquity of this taxon was recently explained by intra-taxon ecological diversification, i.e. specialization of lineages to specific environmental conditions; however, details on specific adaptations are not known. Here we investigated by means of genomic and experimental analyses the ecological adaptation of a persistent population dwelling in a small acidic pond. Findings: The investigated population (F10 lineage) contributed on average 11 % to total bacterioplankton in the pond during the vegetation periods (ice-free period, usually May to November). Only a low degree of genetic diversification of the population could be revealed. These bacteria are characterized by a small genome size (2.1 Mb), a relatively small number of genes involved in transduction of environmental signals, and the lack of motility and quorum sensing. Experiments indicated that these bacteria live as chemoorganotrophs by mainly utilizing low-molecular-weight substrates derived from photooxidation of humic substances. Conclusions: Evolutionary genome streamlining resulted in a highly passive lifestyle so far only known among free-living bacteria from pelagic marine taxa dwelling in environmentally stable nutrient-poor off-shore systems. Surprisingly, such a lifestyle is also successful in a highly dynamic and nutrient-richer environment such as the water column of the investigate

Enrichment of Omnivorous Cercozoan Nanoflagellates from Coastal Baltic Sea Waters

Free-living nano-sized flagellates are important bacterivores in aquatic habitats. However, some slightly larger forms can also be omnivorous, i.e., forage upon both bacterial and eukaryotic resources. This hitherto largely ignored feeding mode may have pronounced implications for the interpretation of experiments about protistan bacterivory. We followed the response of an uncultured group of omnivorous cercozoan nanoflagellates from the Novel Clade 2 (Cerc_BAL02) to experimental food web manipulation in samples from the Gulf of Gdańsk (Southern Baltic Sea). Seawater was either prefiltered through 5 µm filters to exclude larger predators of nanoflagellates (F-treatment), or prefiltered and subsequently 1∶10 diluted with sterile seawater (F+D-treatment) to stimulate the growth of both, flagellates and bacteria. Initially, Cerc_BAL02 were rapidly enriched under both conditions. They foraged on both, eukaryotic prey and bacteria, and were highly competitive at low concentrations of food. However, these omnivores were later only successful in the F+D treatment, where they eventually represented almost one fifth of all aplastidic nanoflagellates. By contrast, their numbers stagnated in the F-treatment, possibly due to top-down control by a concomitant bloom of other, unidentified flagellates. In analogy with observations about the enrichment of opportunistically growing bacteria in comparable experimental setups we suggest that the low numbers of omnivorous Cerc_Bal02 flagellates in waters of the Gulf of Gdańsk might also be related to their vulnerability to grazing pressure

Insect herbivory and herbivores of Ficus species along a rain forest elevational gradient in Papua New Guinea

Classic research on elevational gradients in plant–herbivore interactions holds that insect herbivore pressure is stronger under warmer climates of low elevations. However, recent work has questioned this paradigm, arguing that it oversimplifies the ecological complexity in which plant–insect herbivore interactions are embedded. Knowledge of antagonistic networks of plants and herbivores is however crucial for understanding the mechanisms that govern ecosystem functioning. We examined herbivore damage and insect herbivores of eight species of genus Ficus (105 saplings) and plant constitutive defensive traits of two of these species, along a rain forest elevational gradient of Mt. Wilhelm (200–2,700 m a.s.l.), in tropical Papua New Guinea. We report overall herbivore damage 2.4% of leaf area, ranging from 0.03% in Ficus endochaete at 1,700 m a.s.l. to 6.1% in F. hombroniana at 700 m a.s.l. Herbivore damage and herbivore abundances varied significantly with elevation, as well as among the tree species, and between the wet and dry season. Community‐wide herbivore damage followed a hump‐shaped pattern with the peak between 700 and 1,200 m a.s.l. and this pattern corresponded with abundance of herbivores. For two tree species surveyed in detail, we observed decreasing and hump‐shaped patterns in herbivory, in general matching the trends found in the set of plant defenses measured here. Our results imply that vegetation growing at mid‐elevations of the elevational gradient, that is at the climatically most favorable elevations where water is abundant, and temperatures still relatively warm, suffers the maximum amount of herbivorous damage which changes seasonally, reflecting the water availability

Greenhouse gases from agriculture

The rapidly changing global climate due to increased emission of anthropogenic greenhouse gases (GHGs) is leading to an increased occurrence of extreme weather events such as droughts, floods, and heatwaves. The three major GHGs are carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O). The major natural sources of CO2 include ocean-atmosphere exchange, respiration of animals, soils (microbial respiration) and plants, and volcanic eruption; while the anthropogenic sources include burning of fossil fuel (coal, natural gas, and oil), deforestation, and the cultivation of land that increases the decomposition of soil organic matter and crop and animal residues. Natural sources of CH4 emission include wetlands, termite activities, and oceans. Paddy fields used for rice production, livestock production systems (enteric emission from ruminants), landfills, and the production and use of fossil fuels are the main anthropogenic sources of CH4. Nitrous oxide, in addition to being a major GHG, is also an ozone-depleting gas. N2O is emitted by natural processes from oceans and terrestrial ecosystems. Anthropogenic N2O emissions occur mostly through agricultural and other land-use activities and are associated with the intensification of agricultural and other human activities such as increased use of synthetic fertiliser (119.4 million tonnes of N worldwide in 2019), inefficient use of irrigation water, deposition of animal excreta (urine and dung) from grazing animals, excessive and inefficient application of farm effluents and animal manure to croplands and pastures, and management practices that enhance soil organic N mineralisation and C decomposition. Agriculture could act as a source and a sink of GHGs. Besides direct sources, GHGs also come from various indirect sources, including upstream and downstream emissions in agricultural systems and ammonia (NH3) deposition from fertiliser and animal manure

Micrometeorological methods for greenhouse gas measurement

Micrometeorological techniques are useful if greenhouse gas (GHG) emissions from larger areas (i.e. entire fields) should be integrated. The theory and the various techniques such as flux-gradient, aerodynamic, and Bowen ratio as well as Eddy correlationmethods are described and discussed. Alternativemethods also used areEddy correlation, mass balance techniques, and tracer-based methods.The analytical techniques with current state-of-the-art approaches as well as the calculation procedures are presented

Composition Influences the Pathway but not the Outcome of the Metabolic Response of Bacterioplankton to Resource Shifts

Bacterioplankton community metabolism is central to the functioning of aquatic ecosystems, and strongly reactive to changes in the environment, yet the processes underlying this response remain unclear. Here we explore the role that community composition plays in shaping the bacterial metabolic response to resource gradients that occur along aquatic ecotones in a complex watershed in Québec. Our results show that the response is mediated by complex shifts in community structure, and structural equation analysis confirmed two main pathways, one involving adjustments in the level of activity of existing phylotypes, and the other the replacement of the dominant phylotypes. These contrasting response pathways were not determined by the type or the intensity of the gradients involved, as we had hypothesized, but rather it would appear that some compositional configurations may be intrinsically more plastic than others. Our results suggest that community composition determines this overall level of community plasticity, but that composition itself may be driven by factors independent of the environmental gradients themselves, such that the response of bacterial communities to a given type of gradient may alternate between the adjustment and replacement pathways. We conclude that community composition influences the pathways of response in these bacterial communities, but not the metabolic outcome itself, which is driven by the environment, and which can be attained through multiple alternative configurations

Climate-smart agriculture practices for mitigating greenhouse gas emissions

Agricultural lands make up approximately 37% of the global land surface, and agriculture is a significant source of greenhouse gas (GHG) emissions, including carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O). Those GHGs are responsible for the majority of the anthropogenic globalwarming effect.Agricultural GHG emissions are associated with agricultural soil management (e.g. tillage), use of both synthetic and organic fertilisers, livestock management, burning of fossil fuel for agricultural operations, and burning of agricultural residues and land use change. When natural ecosystems such as grasslands are converted to agricultural production, 20-40% of the soil organic carbon (SOC) is lost over time, following cultivation.We thus need to develop management practices that can maintain or even increase SOC storage in and reduce GHG emissions from agricultural ecosystems. We need to design systematic approaches and agricultural strategies that can ensure sustainable food production under predicted climate change scenarios, approaches that are being called climate-smart agriculture (CSA). Climate-smart agricultural management practices, including conservation tillage, use of cover crops and biochar application to agricultural fields, and strategic application of synthetic and organic fertilisers have been considered a way to reduce GHG emission from agriculture. Agricultural management practices can be improved to decreasing disturbance to the soil by decreasing the frequency and extent of cultivation as a way to minimise soil C loss and/or to increase soil C storage. Fertiliser nitrogen (N) use efficiency can be improved to reduce fertilizer N application and N loss. Management measures can also be taken to minimise agricultural biomass burning. This chapter reviews the current literature on CSA practices that are available to reduce GHG emissions and increase soil C sequestration and develops a guideline on best management practices to reduce GHG emissions, increase C sequestration, and enhance crop productivity in agricultural production systems