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Soils play important roles in biological productivity. While past work suggests that microbes affect soil health and respond to agricultural practices, it is not well known how soil management shapes crop host microbiomes. To elucidate the impact of management on microbial composition and function in the sorghum microbiome, we performed 16S rRNA gene and ITS2 amplicon sequencing and metatranscriptomics on soil and root samples collected from a site in California's San Joaquin Valley that is under long-term cultivation with (i) standard (ST) or no tilling (NT) and (ii) cover cropping (CC) or leaving the field fallow (NO). Our results revealed that microbial diversity, composition, and function change across tillage and cover type, with a heightened response in fungal versus bacterial communities. Surprisingly, ST harbored greater microbial alpha diversity than NT, indicating that tillage may open niche spaces for broad colonization. Across management regimes, we observed class-level taxonomic level shifts. In addition, we found significant functional restructuring across treatments, including enrichment for microbial lipid and carbohydrate transport and metabolism and cell motility with NT. Differences in carbon cycling were also observed, with increased prevalence of glycosyltransferase and glycoside hydrolase carbohydrate active enzyme families with CC. Lastly, treatment significantly influenced arbuscular mycorrhizal fungi, which had the greatest prevalence and activity under ST, suggesting that soil practices mediate known beneficial plant-microbe relationships. Collectively, our results demonstrate how agronomic practices impact critical interactions within the plant microbiome andinformfutureeffortstoconfigure trait-associated microbiomes in crops. [ABSTRACT FROM AUTHOR]

Abstract: Upwelling-favorable winds have increased in most Eastern Boundary Upwelling Systems (EBUS) in the last decades, and it is likely that they increase further in response to global climate change. Here, we explore the response of biological production and air–sea CO2 fluxes to upwelling intensification in two of the four major EBUS, namely the California Current System (California CS) and Canary Current System (Canary CS). To this end, we use eddy-resolving regional ocean models on the basis of the Regional Oceanic Modeling System (ROMS) to which we have coupled a NPZD-type ecosystem model and a biogeochemistry module describing the carbon cycle and subject these model configurations to an idealized increase in the wind stress. We find that a doubling of the wind-stress doubles net primary production (NPP) in the southern California CS and central and northern Canary CS, while it leads to an increase of less than 50% in the central and northern California CS as well as in the southern Canary CS. This differential response is a result of i) different nutrient limitation states with higher sensitivity to upwelling intensification in regions where nutrient limitation is stronger and ii) more efficient nutrient assimilation by biology in the Canary CS relative to the California CS because of a faster nutrient-replete growth rate and longer nearshore water residence times. In the regions where production increases commensurably with upwelling intensification, the enhanced net biological uptake of CO2 compensates the increase in upwelling driven CO2 outgassing, resulting in only a small change in the biological pump efficiency and hence in a small sensitivity of air–sea CO2 fluxes to upwelling intensification. In contrast, in the central California CS as well as in the southern Canary CS around Cape Blanc, the reduced biological efficiency enhances the CO2 outgassing and leads to a substantial sensitivity of the air–sea CO2 fluxes to upwelling intensification. [Copyright &y& Elsevier]

The high biological production of the California Current System (CCS) results from the seasonal development of equatorward alongshore winds that drive coastal upwelling. While several climatic fluctuation patterns influence the dynamics and biological productivity of the CCS, including the El Niño-Southern Oscillation (ENSO), the Pacific Decadal Oscillation index (PDO) and the North Pacific Gyre Oscillation (NPGO), the mechanisms of interaction between climatic oscillations and the CCS upwelling dynamics have remained obscure. Here, we use Singular Spectral Analysis (SSA) to reveal, for the first time, low-frequency concordance between the time series of climatic indices and upwelling intensity along the coast of western North America. Based on energy distributions in annual, semiannual and low-frequency signals, we can divide the coast into three distinct regions. While the annual upwelling signal dominates the energy spectrum elsewhere, low-frequency variability is maximal in the regions south of 33°N. Non-structured variability associated with storms and turbulent mixing is enhanced at northerly locations. We found that the low-frequency signal is significantly correlated with different climatic indices such as PDO, NPGO and ENSO with the correlation patterns being latitude-dependent. We also analyzed the correlations between this upwelling variability and sea surface temperature (SST) and sea level pressure (SLP) throughout the North Pacific to visualize and interpret the large-scale teleconnection dynamics in the atmosphere that drive the low-frequency coastal winds. These results provide new insights into the underlying mechanisms connecting climatic patterns with upwelling dynamics, which could enhance our prediction and forecast capabilities of the effects of future oceanographic and climatic variability in the CCS. [ABSTRACT FROM AUTHOR]

Land use change, natural disturbance, and climate change directly alter ecosystem productivity and carbon stock level. The estimation of ecosystem carbon dynamics depends on the quality of land cover change data and the effectiveness of the ecosystem models that represent the vegetation growth processes and disturbance effects. We used the Integrated Biosphere Simulator (IBIS) and a set of 30- to 60-m resolution fire and land cover change data to examine the carbon changes of California's forests, shrublands, and grasslands. Simulation results indicate that during 1951–2000, the net primary productivity (NPP) increased by 7%, from 72.2 to 77.1TgCyr−1 (1 teragram=1012 g), mainly due to CO2 fertilization, since the climate hardly changed during this period. Similarly, heterotrophic respiration increased by 5%, from 69.4 to 73.1TgCyr−1, mainly due to increased forest soil carbon and temperature. Net ecosystem production (NEP) was highly variable in the 50-year period but on average equalled 3.0TgCyr−1 (total of 149TgC). As with NEP, the net biome production (NBP) was also highly variable but averaged −0.55TgCyr−1 (total of –27.3TgC) because NBP in the 1980s was very low (–5.34TgCyr−1). During the study period, a total of 126Tg carbon were removed by logging and land use change, and 50Tg carbon were directly removed by wildland fires. For carbon pools, the estimated total living upper canopy (tree) biomass decreased from 928 to 834TgC, and the understory (including shrub and grass) biomass increased from 59 to 63TgC. Soil carbon and dead biomass carbon increased from 1136 to 1197TgC. Our analyses suggest that both natural and human processes have significant influence on the carbon change in California. During 1951–2000, climate interannual variability was the key driving force for the large interannual changes of ecosystem carbon source and sink at the state level, while logging and fire were the dominant driving forces for carbon balances in several specific ecoregions. From a long-term perspective, CO2 fertilization plays a key role in maintaining higher NPP. However, our study shows that the increase in C sequestration by CO2 fertilization is largely offset by logging/land use change and wildland fires. [Copyright &y& Elsevier]

Abstract: The Benguela, California, and Humboldt represent three of the major eastern boundary upwelling ecosystems in the world. Upwelling ecosystems are highly productive, and this productivity forms the base of the food chain, potentially leading to ecosystems similar in trophic structure and diversity among upwelling regions. Here we compare the biological and trophic structure of rocky intertidal communities in each of these major upwelling regions. Our comparison includes a fourth region, New Zealand, which spans a similar latitudinal range, and experiences intermittent upwelling. The influence of oceanographic conditions on these communities was evaluated by using the long-term mean and standard deviation of satellite-based sea surface temperature (SST). Large differences emerged in the taxonomic richness in each of these systems, with California as the most and the Humboldt as the least taxonomically rich. Across all regions, richness tended to decrease progressively from lower trophic levels (macrophytes) to higher trophic levels (carnivores), and richness was inversely correlated with the proportion of variance in SST contained in the seasonal cycle, suggesting that strongly seasonal, predictable environments are relatively low in diversity. The functional and trophic structures were remarkably similar across these four regions of the world. Macrophytes were slightly dominant over filter-feeders in terms of space occupancy in all regions except the Benguela. Densities of herbivorous grazers were greatest in California and Benguela and far outnumbered carnivore densities in all regions. Despite some similarities, the overall structure of the communities from these regions differed significantly supporting the hypothesis that the biological and ecological consequences of similar physical forcing mechanisms (e.g. upwelling) are likely to be context-dependent. [Copyright &y& Elsevier]

The article presents a study which discusses the abundance and distribution of demersal fishes found on three seamounts off Central and Southern California. It mentions that the researchers used video observations taken during 27 dives of a remotely operated vehicle (ROV), which were analyzed to quantify organism density. It relates that having knowledge on the biogeographic patterns and baseline assessments of seamount fish assemblages is important in establishing management and policy guidelines among fisheries.

This article examines arguments about the relationship between mainstream agriculture and alternative food chains. It begins with a summary of Guthman's study of organic agriculture in California and her conclusion that it has come to resemble conventional, industrial agriculture in its agrarian structures and its supply chains. The article raises questions about both the evidence that smaller alternative producers have been squeezed out, and the assumptions underlying the analysis of relations between capitalist and non-capitalist forms. The issues are contextualized through a summary of earlier debates about the fate of non-capitalist producers in the ‘development’ process, and through reference to studies in economic anthropology, including research on household farming strategies in Italy. The article concludes that alternative food chains do not follow a simple linear trajectory, and that we need to include an ethnographic approach to understand both their economic values and political objectives. [ABSTRACT FROM AUTHOR]

The significance of the transport of nutrient-rich hypolimnetic water via the benthic boundary layer (BBL) to the productivity of Mono Lake was studied using a coupled hydrodynamic and ecological model validated against field data. The coupled model enabled us to differentiate between the role of biotic components and hydrodynamic forcing on the internal recycling of nutrients necessary to sustain primary productivity. A 4-year period (1991-1994) was simulated in which recycled nutrients from zooplankton excretion and bacterially-mediated mineralization exceeded sediment fluxes as the dominant source for primary productivity. Model outputs indicated that BBL transport was responsible for a 53% increase in the flux of hypolimnetic ammonium to the photic zone during stratification with an increase in primary production of 6% and secondary production of 5%. Although the estimated impact of BBL transport on the productivity of Mono Lake was not large, significant nutrient fluxes were simulated during periods when BBL transport was most active. [ABSTRACT FROM AUTHOR]

The stomachs of 130 sandpaper skates, Bathyraja kincaidii (Garman, 1908), were sampled from off central California to determine their diet composition. The overall diet was dominated by euphausiids, but shrimps, polychaetes and squids were also important secondary prey. A three-factor MANOVA demonstrated significant differences in the diet by sex, maturity status and oceanographic season using numeric and gravimetric measures of importance for the major prey categories. These three main factors explained more variation in diet than interactions between the factors, and season explained the most variance overall. A detailed analysis of the seasonal variation among the prey categories indicated that abundance changes in the most important prey, euphausiids, were coupled with seasonal changes in the importance of other prey. When upwelling occurred and productivity was great (Upwelling and Oceanic seasons), euphausiids were likely highly abundant in the study area and were the most important prey for B. kincaidii. As productivity declined (Davidson Current season), euphausiids appeared to decrease in abundance and B. kincaidii switched to secondary prey. At that time, gammarid amphipods and shrimps became the most important prey items and polychaetes, mysids and euphausiids were secondary. [ABSTRACT FROM AUTHOR]

Abstract: The substantial inventory of nitrate (NO3) in San Francisco Bay (SFB) is unavailable to the resident phytoplankton most of the year due to the presence of ammonium (NH4) at inhibitory concentrations that prevents NO3 uptake. Low annual primary productivity in this turbid estuary is generally attributed to the poor irradiance conditions. However, this may not be the only cause; spring phytoplankton blooms occur irregularly in north SFB only when NH4 concentrations are low, <4μmolL−1 and NO3 uptake by phytoplankton occurs. Field measurements and enclosure experiments confirm the NH4 inhibition process to be the cause of low NO3 utilization most of the year. Detailed analysis of spring blooms in three embayments of SFB over 3 years shows a consistent sequence of events that result in bursts of chlorophyll. The first requirement is improved irradiance conditions through stabilization of the water column by stratification or reduced tidal activity. Second, NH4 concentrations must be reduced to a critical range, 1 to 4μmolL−1 through dilution by precipitation and by phytoplankton uptake. This enables rapid uptake of NO3 and subsequent increase in chlorophyll. The resulting bloom is due to both the initial uptake of NH4 and the subsequent uptake of NO3. The NO3 uptake step is crucial since it is the larger nitrogen source and uptake occurs at higher rates than that for NH4 at the concentrations that occur in SFB. Existing models of light-limited, non-nutrient limited productivity in SFB require modification to include the NH4 inhibition effect. From measured NH4 uptake rates and initial concentrations, calculations can be made to predict the length of time that favorable irradiance conditions are required for the phytoplankton population to reduce ambient NH4 concentrations to non-inhibiting concentrations and allow bloom formation to begin. For Suisun Bay, the time required is so long that blooms are unlikely in any season. For San Pablo and Central Bays, these times are too long in summer but sufficiently short in spring to allow bloom development, depending on the ambient NH4 concentration prior to the productivity season. NH4 sources to SFB are primarily anthropogenic, from agricultural drainage and sewage treatment plants, and if not sufficiently diluted by runoff and precipitation can prevent development of the spring phytoplankton bloom. Attention should be paid to the form of N making up dissolved inorganic nitrogen (DIN) in nutrient-rich estuaries. [Copyright &y& Elsevier]

Abstract: Large aquatic bodies influence surrounding terrestrial ecosystems by providing water and nutrients. In arid landscapes, the increased primary productivity that results may greatly enhance vertebrate biodiversity. The Salton Sea, a large saline lake in the Colorado Desert of southern California, provides nutrients in the form of hundreds of thousands of dead fish carcasses, brine flies, and chemical compounds through windborne salt sea spray. We performed point counts for landbirds and shorebirds monthly or every other month between March 2001 and February 2002 across a sampling grid of 35 points along the west edge of Salton Sea. We found that avian diversity (numbers of species and numbers per species) was dependent on proximity to the Sea. Diversity was at a maximum nearest the shore, and was significantly lower away from the Sea''s edge, at all surveyed distances up to 1km from the shore. Cover by the dominant shrubs on the study site also corresponded to proximity to the water''s edge. Whereas one may hypothesize that the avian diversity patterns are caused by these differences in vegetation structure, our data did not support this. Future studies should further investigate this potential correlation between vegetation and bird patterns. Until more is understood about the relationship between elevated avian diversity and the physical environment of the land-shore interface, our results suggest that the Sea''s surface be stabilized near its present level. Future management schemes at the Salton Sea that include reductions of water sources should be carefully analyzed, so as to not jeopardize the terrestrial avifauna at this unique ecosystem. [Copyright &y& Elsevier]