Differential impact of top-down and bottom-up forces in structuring freshwater bacterial communities

Microplastics alter the functioning of marine microbial ecosystems

Microplastics pervade ocean ecosystems. Despite their effects on individuals or populations are well documented, the consequences of microplastics on ecosystem functioning are still largely unknown. Here, we show how microplastics alter the structure and functioning of pelagic microbial ecosystems. Using experimental pelagic mesocosms, we found that microplastics indirectly affect marine productivity by changing the bacterial and phytoplankton assemblages. Specifically, the addition of microplastics increased phytoplankton biomass and shifted bacterial assemblages' composition. Such changes altered the interactions between heterotrophic and autotrophic microbes and the cycling of ammonia in the water column, which ultimately benefited photosynthetic efficiency. The effects of microplastics on marine productivity were consistent for different microplastic types. This study demonstrates that microplastics affect bacteria and phytoplankton communities and influence marine productivity, which ultimately alters the functioning of the whole ocean ecosystem.

Roles of high/low nucleic acid bacteria in flocs and probing their dynamic migrations with respirogram

Bacterial migration is crucial for the stability of activated sludge but rarely reported. The static distribution was explored by changes in bacteria concentration with extracellular polymeric substances (EPS) extractions. Next, denitrification and aeration were conducted as normal running conditions for examining the bacterial migration between floc-attached and dispersed growth. Above observations were further explored by conducting copper ion (Cu2+) shock as an extreme running condition. After extracting EPS, low nucleic acid (LNA) bacteria migrated from the sludge to the supernatant primarily, and high nucleic acid (HNA) bacteria remained in the residual sludge, suggesting that HNA bacteria mainly distributed inside the sludge while LNA bacteria outside the sludge. During the denitrification process, LNA bacteria migrated out of flocs, which increased by 6.94 × 106 events/mL in the supernatant. During the feast phase of aeration, LNA bacteria grew attached to flocs, causing the increased flocs diameter from 45.60 to 47.40 μm. During the following aerobic famine phase, LNA bacteria grew dispersedly, but HNA bacteria remained unchanged. However, a further severe famine phase drove HNA bacteria to be dispersed, breaking flocs with the decreased diameter from 48.10 to 46.50 μm. When the Cu2+ shock was employed, LNA and HNA bacteria increased but the LNA/HNA ratio decreased in the supernatant, indicating more HNA bacteria migrating to the dispersed phase. From a structural perspective, HNA bacteria distributed inside the sludge and functioned as the backbone of flocs, undertaking the maintenance of flocs stability primarily; while LNA bacteria distributed outside the sludge and functioned as filling materials, having a secondary influence on flocs stability. These processes were also probed by respirogram exactly, correlating the system-scale measurement and microscale migrations and providing an early warning signal under abnormal circumstances. The processed HNA-backbone theory is promising for regulating the stability of activated sludge based on bacterial migrations.

Top-Down Controls of Bacterial Metabolism: A Case Study from a Temperate Freshwater Lake Ecosystem

In freshwater environments, limited data exist on the impact of mortality forces (viruses and heterotrophic nanoflagellates) on bacterial growth efficiency (BGE, index of bacterial carbon metabolism) compared to resource availability. An investigation to determine the relative influence of viral lysis and flagellate predation (top-down forces) on BGE was conducted in a mesotrophic freshwater system (Lake Goule, France) with time and space. Viral abundance was significantly (p < 0.001) related to bacterial abundance by a power law function with an exponent less than 1, emphasizing that the increases in host population (bacteria) together with viruses were not proportionate. A lytic viral strategy was evident throughout the study period, with high lysis of the bacterial population (up to 60%) supported by viral production rates. Viral processes (lysis and production) that were influenced by bacterial production and heterotrophic nanoflagellate abundance had a positive impact on BGE. Estimates of BGE were variable (9.9−45.5%) due to uncoupling between two metabolic parameters—namely bacterial production and respiration. The existence of a synergistic relationship between viruses and flagellates with bacteria in Lake Goule highlighted the decisive impact of top-down agents in sustaining the bacterial carbon metabolism of non-infected population through the nature of vital resources released via mortality processes.

Phage strategies facilitate bacterial coexistence under environmental variability

Bacterial communities are often exposed to temporal variations in resource availability, which exceed bacterial generation times and thereby affect bacterial coexistence. Bacterial population dynamics are also shaped by bacteriophages, which are a main cause of bacterial mortality. Several strategies are proposed in the literature to describe infections by phages, such as "Killing the Winner", "Piggyback the loser" (PtL) or "Piggyback the Winner" (PtW). The two temperate phage strategies PtL and PtW are defined by a change from lytic to lysogenic infection when the host density changes, from high to low or from low to high, respectively. To date, the occurrence of different phage strategies and their response to environmental variability is poorly understood. In our study, we developed a microbial trophic network model using ordinary differential equations (ODEs) and performed 'in silico' experiments. To model the switch from the lysogenic to the lytic cycle, we modified the lysis rate of infected bacteria and their growth was turned on or off using a density-dependent switching point. We addressed whether and how the different phage strategies facilitate bacteria coexistence competing for limiting resources. We also studied the impact of a fluctuating resource inflow to evaluate the response of the different phage strategies to environmental variability. Our results show that the viral shunt (i.e. nutrient release after bacterial lysis) leads to an enrichment of the system. This enrichment enables bacterial coexistence at lower resource concentrations. We were able to show that an established, purely lytic model leads to stable bacterial coexistence despite fluctuating resources. Both temperate phage models differ in their coexistence patterns. The model of PtW yields stable bacterial coexistence at a limited range of resource supply and is most sensitive to resource fluctuations. Interestingly, the purely lytic phage strategy and PtW both result in stable bacteria coexistence at oligotrophic conditions. The PtL model facilitates stable bacterial coexistence over a large range of stable and fluctuating resource inflow. An increase in bacterial growth rate results in a higher resilience to resource variability for the PtL and the lytic infection model. We propose that both temperate phage strategies represent different mechanisms of phages coping with environmental variability. Our study demonstrates how phage strategies can maintain bacterial coexistence in constant and fluctuating environments.