Resilience of the Natural Phyllosphere Microbiota of the Grapevine to Chemical and Biological Pesticides

ABSTRACTThe phyllosphere is colonized by complex microbial communities, which are adapted to the harsh habitat. Although the role and ecology of nonpathogenic microorganisms of the phyllosphere are only partially understood, leaf microbiota could have a beneficial role in plant growth and health. Pesticides and biocontrol agents are frequently applied to grapevines, but the impact on nontarget microorganisms of the phyllosphere has been marginally considered. In this study, we investigated the effect of a chemical fungicide (penconazole) and a biological control agent (Lysobacter capsiciAZ78) on the leaf microbiota of the grapevine at three locations. Amplicons of the 16S rRNA gene and of the internal transcribed spacer were sequenced for bacterial and fungal identification, respectively. Pyrosequencing analysis revealed that the richness and diversity of bacterial and fungal populations were only minimally affected by the chemical and biological treatments tested, and they mainly differed according to grapevine locations. Indigenous microbial communities of the phyllosphere are adapted to environmental and biotic factors in the areas where the grapevines are grown, and they are resilient to the treatments tested. The biocontrol properties of phyllosphere communities against downy mildew differed among grapevine locations and were not affected by treatments, suggesting that biocontrol communities could be improved with agronomic practices to enrich beneficial populations in vineyards.

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Influence of Fishmeal-Free Diets on Microbial Communities in Atlantic Salmon (Salmo salar) Recirculation Aquaculture Systems

Applied and Environmental Microbiology ◽

10.1128/aem.00902-16 ◽

2016 ◽

Vol 82 (15) ◽

pp. 4470-4481 ◽

Cited By ~ 55

Author(s):

Victor Schmidt ◽

Linda Amaral-Zettler ◽

John Davidson ◽

Steven Summerfelt ◽

Christopher Good

Keyword(s):

Water Quality ◽

Atlantic Salmon ◽

Microbial Communities ◽

Salmo Salar ◽

Rrna Gene ◽

Fish Diet ◽

Content Type ◽

Recirculating Aquaculture Systems ◽

Alternative Feeds ◽

The Impact

ABSTRACTReliance on fishmeal as a primary protein source is among the chief economic and environmental concerns in aquaculture today. Fishmeal-based feeds often require harvest from wild fish stocks, placing pressure on natural ecosystems and causing price instability. Alternative diet formulations without the use of fishmeal provide a potential solution to this challenge. Although the impact of alternative diets on fish performance, intestinal inflammation, palatability, and gut microbiota has been a topic of recent interest, less is known about how alternative feeds impact the aquaculture environment as a whole. The recent focus on recirculating aquaculture systems (RAS) and the closed-containment approach to raising food fish highlights the need to maintain stable environmental and microbiological conditions within a farm environment. Microbial stability in RAS biofilters is particularly important, given its role in nutrient processing and water quality in these closed systems. If and how the impacts of alternative feeds on microbial communities in fish translate into changes to the biofilters are not known. We tested the influence of a fishmeal-free diet on the microbial communities in RAS water, biofilters, and salmon microbiomes using high-throughput 16S rRNA gene V6 hypervariable region amplicon sequencing. We grew Atlantic salmon (Salmo salar) to market size in six replicate RAS tanks, three with traditional fishmeal diets and three with alternative-protein, fishmeal-free diets. We sampled intestines and gills from market-ready adult fish, water, and biofilter medium in each corresponding RAS unit. Our results provide data on how fish diet influences the RAS environment and corroborate previous findings that diet has a clear influence on the microbiome structure of the salmon intestine, particularly within the orderLactobacillales(lactic acid bacteria). We conclude that the strong stability of taxa likely involved in water quality processing regardless of diet (e.g.,Nitrospira) may further alleviate concerns regarding the use of alternative feeds in RAS operations.IMPORTANCEThe growth of the aquaculture industry has outpaced terrestrial livestock production and wild-capture fisheries for over 2 decades, currently producing nearly 50% of all seafood consumed globally. As wild-capture fisheries continue to decline, aquaculture's role in food production will grow, and it will produce an estimated 62% of all seafood consumed in 2020. A significant environmental concern of the industry is the reliance on fishmeal as a primary feed ingredient, as its production still requires harvest from wild fisheries. Our study adds to the growing body of literature on the feasibility of alternative, fishmeal-free diets. Specifically, we asked how fishmeal-free diets influence microbial communities in recirculating salmon farms. Unlike previous studies, we extended our investigation beyond the microbiome of the fish itself and asked how alterative diets influence microbial communities in water and critical biofilter habitats. We found no evidence for adverse effects of alternative diets on any microbial habitat within the farm.

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Microbial drivers of methane emissions from unrestored industrial salt ponds

The ISME Journal ◽

10.1038/s41396-021-01067-w ◽

2021 ◽

Author(s):

Jinglie Zhou ◽

Susanna M. Theroux ◽

Clifton P. Bueno de Mesquita ◽

Wyatt H. Hartman ◽

Ye Tian ◽

...

Keyword(s):

Microbial Communities ◽

Methane Flux ◽

Methane Emissions ◽

Metagenomic Data ◽

Rrna Gene ◽

Salt Ponds ◽

Salt Pond ◽

Reference Wetlands ◽

Reference Wetland ◽

The Impact

AbstractWetlands are important carbon (C) sinks, yet many have been destroyed and converted to other uses over the past few centuries, including industrial salt making. A renewed focus on wetland ecosystem services (e.g., flood control, and habitat) has resulted in numerous restoration efforts whose effect on microbial communities is largely unexplored. We investigated the impact of restoration on microbial community composition, metabolic functional potential, and methane flux by analyzing sediment cores from two unrestored former industrial salt ponds, a restored former industrial salt pond, and a reference wetland. We observed elevated methane emissions from unrestored salt ponds compared to the restored and reference wetlands, which was positively correlated with salinity and sulfate across all samples. 16S rRNA gene amplicon and shotgun metagenomic data revealed that the restored salt pond harbored communities more phylogenetically and functionally similar to the reference wetland than to unrestored ponds. Archaeal methanogenesis genes were positively correlated with methane flux, as were genes encoding enzymes for bacterial methylphosphonate degradation, suggesting methane is generated both from bacterial methylphosphonate degradation and archaeal methanogenesis in these sites. These observations demonstrate that restoration effectively converted industrial salt pond microbial communities back to compositions more similar to reference wetlands and lowered salinities, sulfate concentrations, and methane emissions.

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Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters

Applied and Environmental Microbiology ◽

10.1128/aem.03001-13 ◽

2013 ◽

Vol 80 (1) ◽

pp. 177-183 ◽

Cited By ~ 10

Author(s):

Lavane Kim ◽

Eulyn Pagaling ◽

Yi Y. Zuo ◽

Tao Yan

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Bacterial Species ◽

Community Analysis ◽

Microbial Community Analysis ◽

Rrna Gene ◽

Content Type ◽

Property Change ◽

And Control ◽

Start Ups

ABSTRACTThe impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected,BurkholderialesandRhodocyclalesof theBetaproteobacteriaclass were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes.

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Differences in the Rumen Methanogen Populations of Lactating Jersey and Holstein Dairy Cows under the Same Diet Regimen

Applied and Environmental Microbiology ◽

10.1128/aem.05130-11 ◽

2011 ◽

Vol 77 (16) ◽

pp. 5682-5687 ◽

Cited By ~ 64

Author(s):

Erin E. King ◽

Rachel P. Smith ◽

Benoit St-Pierre ◽

André-Denis G. Wright

Keyword(s):

Methanogenic Archaea ◽

Milk Composition ◽

Species Level ◽

Rrna Gene ◽

Content Type ◽

Sequence Identity ◽

Diet Regimen ◽

Pcr Products ◽

The Impact ◽

Rumen Methanogen

ABSTRACTIn the dairy cattle industry, Holstein and Jersey are the breeds most commonly used for production. They differ in performance by various traits, such as body size, milk production, and milk composition. With increased concerns about the impact of agriculture on climate change, potential differences in other traits, such as methane emission, also need to be characterized further. Since methane is produced in the rumen by methanogenic archaea, we investigated whether the population structure of methanogen communities would differ between Holsteins and Jerseys. Breed-specific rumen methanogen 16S rRNA gene clone libraries were constructed from pooled PCR products obtained from lactating Holstein and Jersey cows, generating 180 and 185 clones, respectively. The combined 365 sequences were assigned to 55 species-level operational taxonomic units (OTUs). Twenty OTUs, representing 85% of the combined library sequences, were common to both breeds, while 23 OTUs (36 sequences) were found only in the Holstein library and 12 OTUs (18 sequences) were found only in the Jersey library, highlighting increased diversity in the Holstein library. Other differences included the observation that sequences with species-like sequence identity toMethanobrevibacter milleraewere represented more highly in the Jersey breed, whileMethanosphaera-related sequences and novel uncultured methanogen clones were more frequent in the Holstein library. In contrast, OTU sequences with species-level sequence identity toMethanobrevibacter ruminantiumwere represented similarly in both libraries. Since the sampled animals were from a single herd consisting of two breeds which were fed the same diet and maintained under the same environmental conditions, the differences we observed may be due to differences in host breed genetics.

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Shaping of the Present-Day Deep Biosphere at Chicxulub by the Impact Catastrophe That Ended the Cretaceous

Frontiers in Microbiology ◽

10.3389/fmicb.2021.668240 ◽

2021 ◽

Vol 12 ◽

Author(s):

Charles S. Cockell ◽

Bettina Schaefer ◽

Cornelia Wuchter ◽

Marco J. L. Coolen ◽

Kliti Grice ◽

...

Keyword(s):

Microbial Communities ◽

Amplicon Sequencing ◽

Granitic Rocks ◽

Rrna Gene ◽

Deep Biosphere ◽

Deep Subsurface ◽

Cell Biomass ◽

Colonization Potential ◽

The Impact

We report on the effect of the end-Cretaceous impact event on the present-day deep microbial biosphere at the impact site. IODP-ICDP Expedition 364 drilled into the peak ring of the Chicxulub crater, México, allowing us to investigate the microbial communities within this structure. Increased cell biomass was found in the impact suevite, which was deposited within the first few hours of the Cenozoic, demonstrating that the impact produced a new lithological horizon that caused a long-term improvement in deep subsurface colonization potential. In the biologically impoverished granitic rocks, we observed increased cell abundances at impact-induced geological interfaces, that can be attributed to the nutritionally diverse substrates and/or elevated fluid flow. 16S rRNA gene amplicon sequencing revealed taxonomically distinct microbial communities in each crater lithology. These observations show that the impact caused geological deformation that continues to shape the deep subsurface biosphere at Chicxulub in the present day.

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Extracellular Enzyme Activity and Microbial Diversity Measured on Seafloor Exposed Basalts from Loihi Seamount Indicate the Importance of Basalts to Global Biogeochemical Cycling

Applied and Environmental Microbiology ◽

10.1128/aem.01038-14 ◽

2014 ◽

Vol 80 (16) ◽

pp. 4854-4864 ◽

Cited By ~ 18

Author(s):

Myrna E. Jacobson Meyers ◽

Jason B. Sylvan ◽

Katrina J. Edwards

Keyword(s):

Enzyme Activity ◽

Microbial Communities ◽

Enzyme Activities ◽

Leucine Aminopeptidase ◽

Extracellular Enzyme ◽

Basaltic Rock ◽

Rrna Gene ◽

Content Type ◽

Shelf Sediments ◽

Potential Enzyme Activity

ABSTRACTSeafloor basalts are widely distributed and host diverse prokaryotic communities, but no data exist concerning the metabolic rates of the resident microbial communities. We present here potential extracellular enzyme activities of leucine aminopeptidase (LAP) and alkaline phosphatase (AP) measured on basalt samples from different locations on Loihi Seamount, HI, coupled with analysis of prokaryotic biomass and pyrosequencing of the bacterial 16S rRNA gene. The community maximum potential enzyme activity (Vmax) of LAP ranged from 0.47 to 0.90 nmol (g rock)−1h−1; theVmaxfor AP was 28 to 60 nmol (g rock)−1h−1. TheKmof LAP ranged from 26 to 33 μM, while theKmfor AP was 2 to 7 μM. Bacterial communities on Loihi basalts were comprised primarily ofAlpha-,Delta-, andGammaproteobacteria,Bacteroidetes, andPlanctomycetes. The putative ability to produce LAP is evenly distributed across the most commonly detected bacterial orders, but the ability to produce AP is likely dominated by bacteria in the ordersXanthomonadales,Flavobacteriales, andPlanctomycetales. The enzyme activities on Loihi basalts were compared to those of other marine environments that have been studied and were found to be similar in magnitude to those from continental shelf sediments and orders of magnitude higher than any measured in the water column, demonstrating that the potential for exposed basalts to transform organic matter is substantial. We propose that microbial communities on basaltic rock play a significant, quantifiable role in benthic biogeochemical processes.

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Biological Control of the Weedy Plant (Rumex crispus) at the Seedling Growth Stage by the Green Dock Beetle (Gastrophysa viridula)

Journal of King Abdulaziz University-Meteorology Environment and Arid Land Agriculture Sciences ◽

10.4197/met.28-1.3 ◽

2019 ◽

Vol 28 (1) ◽

pp. 21-31

Author(s):

Khalid S. Alshallash Khalid S. Alshallash

Keyword(s):

Biological Control ◽

Seedling Growth ◽

Growth Stage ◽

Biological Control Agent ◽

Dry Weight ◽

Control Agent ◽

Growth Stages ◽

Rumex Crispus ◽

Shoot Number ◽

The Impact

In four glasshouse experiments, the effectiveness of the adult green dock beetle Gastrophysa viridula (Coleoptera: Chrysomelidae), at the effective number of applied individuals, for use as a biological control agent of curled dock, Rumex crispus (Polygonaceae) were studied. The feeding of the beetle was investigated at four different numbers of beetle (0, 1, 2, 3) and at four seedling growth stages of the plant, defined by the average of leaf area per plant (1-1.22 , 2-4.45, 3-11.56, and 4-71.52 cm2/plant). Grazing by one, two or three dock beetles did not result in a significant reduction in dock dry weight or shoot numbers at the youngest growth stage. However, both at later seedling growth stages were significantly affected (P ? 0.0001), at any beetles number. The increase of beetle numbers caused nonsignificant increased effect, in some trials, confirming the impact of a single beetle. Three months after beetle grazing, dock seedlings of first, second and third growth stages were not able to regrow, however, some plants at the 4th growth stage, re-emerged. This suggested that the highest effect of beetle's feeding occurs on the early seedling stages. Statistical analysis showed a positive correlation (0.77) between dry weight and shoot number at all the four seedling growth stages, thus confirming the impact of the beetle on both the dry weight and shoot numbers. Combining beetle grazing with other control methods at older dock seedling stages could, therefore, provide better suppression

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Repeated Anaerobic Microbial Redox Cycling of Iron

Applied and Environmental Microbiology ◽

10.1128/aem.00276-11 ◽

2011 ◽

Vol 77 (17) ◽

pp. 6036-6042 ◽

Cited By ~ 103

Author(s):

Aaron J. Coby ◽

Flynn Picardal ◽

Evgenya Shelobolina ◽

Huifang Xu ◽

Eric E. Roden

Keyword(s):

Microbial Communities ◽

Microscopic Analysis ◽

Redox Cycling ◽

Most Probable Number ◽

Rrna Gene ◽

Electron Microscopic ◽

16S Rrna Gene Analysis ◽

Probable Number ◽

Content Type ◽

Floodplain Sediments

ABSTRACTSome nitrate- and Fe(III)-reducing microorganisms are capable of oxidizing Fe(II) with nitrate as the electron acceptor. This enzymatic pathway may facilitate the development of anaerobic microbial communities that take advantage of the energy available during Fe-N redox oscillations. We examined this phenomenon in synthetic Fe(III) oxide (nanocrystalline goethite) suspensions inoculated with microflora from freshwater river floodplain sediments. Nitrate and acetate were added at alternate intervals in order to induce repeated cycles of microbial Fe(III) reduction and nitrate-dependent Fe(II) oxidation. Addition of nitrate to reduced, acetate-depleted suspensions resulted in rapid Fe(II) oxidation and accumulation of ammonium. High-resolution transmission electron microscopic analysis of material from Fe redox cycling reactors showed amorphous coatings on the goethite nanocrystals that were not observed in reactors operated under strictly nitrate- or Fe(III)-reducing conditions. Microbial communities associated with N and Fe redox metabolism were assessed using a combination of most-probable-number enumerations and 16S rRNA gene analysis. The nitrate-reducing and Fe(III)-reducing cultures were dominated by denitrifyingBetaproteobacteria(e.g.,Dechloromonas) and Fe(III)-reducingDeltaproteobacteria(Geobacter), respectively; these same taxa were dominant in the Fe cycling cultures. The combined chemical and microbiological data suggest that bothGeobacterand variousBetaproteobacteriaparticipated in nitrate-dependent Fe(II) oxidation in the cycling cultures. Microbially driven Fe-N redox cycling may have important consequences for both the fate of N and the abundance and reactivity of Fe(III) oxides in sediments.

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Corrigendum to: The impact of rabbit haemorrhagic disease on wild rabbit (Oryctolagus cuniculus) populations in Queensland

Wildlife Research ◽

10.1071/wr00099_co ◽

2004 ◽

Vol 31 (6) ◽

pp. 651

Author(s):

G. Story ◽

J. Scanlan ◽

R. Palmer ◽

D. Berman

Keyword(s):

Biological Control Agent ◽

South Australia ◽

Control Agent ◽

Wild Rabbit ◽

Isolated Populations ◽

Rabbit Haemorrhagic Disease ◽

Northern Edge ◽

The Mean ◽

Haemorrhagic Disease ◽

The Impact

Rabbit haemorrhagic disease virus (RHDV) escaped from quarantine facilities on Wardang Island in September 1995 and spread through South Australia to Queensland by December 1995. To determine the impact of this biological control agent on wild rabbit populations in Queensland, shot sample and spotlight count data were collected at six sites. RHDV spread across Queensland from the south-west to the east at a rate of at least 91 km month–1 between October 1995 and October 1996. The initial impact on rabbit density appeared highly variable, with an increase of 81% (255 ± 79 (s.e.) to 385 ± 73 rabbits km–2) at one site and a decrease of 83% (129 ± 27 to 22 ± 18 rabbits km–2) at another during the first outbreak. However, after 30 months of RHDV activity, counts were at least 90% below counts conducted before RHDV arrived. Using a population model to account for environmental conditions, the mean suppression of rabbit density caused by rabbit haemorrhagic disease (RHD) was estimated to be 74% (ranging from 43% to 94% between sites). No outbreaks were observed when the density of susceptible rabbits was lower than 12 km–2. Where rabbit density remains low for long periods RHDV may not persist. This is perhaps most likely to occur in the isolated populations towards the northern edge of the range of rabbits in Australia. RHDV may have to be reintroduced into these populations. Further south in areas more suitable for rabbits, RHDV is more likely to persist, resulting in a high density of immune rabbits. In such areas conventional control techniques may be more important to enhance the influence of RHD.

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Water management and phenology influence the root-associated rice field microbiota

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa146 ◽

2020 ◽

Vol 96 (9) ◽

Author(s):

Matteo Chialva ◽

Stefano Ghignone ◽

Paolo Cozzi ◽

Barbara Lazzari ◽

Paola Bonfante ◽

...

Keyword(s):

Water Management ◽

Microbial Communities ◽

Rice Field ◽

Water Status ◽

18S Rrna Gene ◽

Rrna Gene ◽

Upland Conditions ◽

The Impact ◽

Comprehensive Study

ABSTRACT Microbial communities associated with plants are greatly influenced by water availability in soil. In flooded crops, such as rice, the impact of water management on microbial dynamics is not fully understood. Here, we present a comprehensive study of the rice microbiota investigated in an experimental field located in one of the most productive areas of northern Italy. The microbiota associated with paddy soil and root was investigated using 454 pyrosequencing of 16S, ITS and 18S rRNA gene amplicons under two different water managements, upland (non-flooded, aerobic) and lowland (traditional flooding, anaerobic), at three plant development stages. Results highlighted a major role of the soil water status in shaping microbial communities, while phenological stage had low impacts. Compositional shifts in prokaryotic and fungal communities upon water management consisted in significant abundance changes of Firmicutes, Methanobacteria, Chloroflexi, Sordariomycetes, Dothideomycetes and Glomeromycotina. A vicariance in plant beneficial microbes and between saprotrophs and pathotrophs was observed between lowland and upland. Moreover, through network analysis, we demonstrated different co-abundance dynamics between lowland and upland conditions with a major impact on microbial hubs (strongly interconnected microbes) that fully shifted to aerobic microbes in the absence of flooding.

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